Rice cultivar Calaroma-201

ABSTRACT

A rice cultivar designated Calaroma-201 is disclosed. The invention relates to the seeds of rice cultivar Calaroma-201, to the plants of rice Calaroma-201 and to methods for producing a rice plant produced by crossing the cultivar Calaroma-201 with itself or another rice variety. The invention further relates to methods for producing a rice plant containing in its genetic material one or more transgenes and to the transgenic rice plants and plant parts produced by those methods. This invention also relates to rice cultivars or breeding cultivars and plant parts derived from rice cultivar Calaroma-201, to methods for producing other rice cultivars, lines or plant parts derived from rice cultivar Calaroma-201 and to the rice plants, varieties, and their parts derived from the use of those methods. The invention further relates to hybrid rice seeds and plants produced by crossing the cultivar Calaroma-201 with another rice cultivar.

BACKGROUND OF THE INVENTION

The present invention relates to a new and distinctive rice cultivardesignated Calaroma-201. All publications cited in this application areherein incorporated by reference.

Rice is an ancient agricultural crop and is today one of the principalfood crops of the world. There are two cultivated species of rice: Oryzasativa L., the Asian rice, and O. glaberrima Steud., the African rice.O. sativa L. constitutes virtually all of the world's cultivated riceand is the species grown in the United States. Three major riceproducing regions exist in the United States: the Mississippi Delta(Arkansas, Mississippi, northeast Louisiana, southeast Missouri), theGulf Coast (southwest Louisiana, southeast Texas), and the CentralValleys of California.

Rice is a semi-aquatic crop that benefits from flooded soil conditionsduring part or all of the growing season. In the United States, rice isgrown on flooded soils to optimize grain yields. Heavy clay soils orsilt loam soils with hard pan layers about 30 cm below the surface aretypical rice-producing soils because they minimize water losses fromsoil percolation. Rice production in the United States can be broadlycategorized as either dry-seeded or water-seeded. In the dry-seededsystem, rice is sown into a well-prepared seed bed with a grain drill orby broadcasting the seed and incorporating it with a disk or harrow.Moisture for seed germination is from irrigation or rainfall. For thedry-seeded system, when the plants have reached sufficient size (four-to five-leaf stage), a shallow permanent flood of water 5 to 16 cm deepis applied to the field for the remainder of the crop season.

In the water-seeded system, rice seed is soaked for 12 to 36 hours toinitiate germination, and the seed is broadcast by airplane into aflooded field. The seedlings emerge through a shallow flood, or thewater may be drained from the field for a short period of time toenhance seedling establishment. A shallow flood is maintained until therice approaches maturity. For both the dry-seeded and water-seededproduction systems, the fields are drained when the crop is mature, andthe rice is harvested 2 to 3 weeks later with large combines. In ricebreeding programs, breeders try to employ the production systemspredominant in their respective region. Thus, a drill-seeded breedingnursery is used by breeders in a region where rice is drill-seeded and awater-seeded nursery is used in regions where water-seeding isimportant.

Rice in the United States is classified into three primary market typesby grain size, shape, and chemical composition of the endosperm:long-grain, medium grain and short-grain. Typical U. S. long-graincultivars cook dry and fluffy when steamed or boiled, whereas medium-and short-grain cultivars cook moist and sticky. Long-grain cultivarshave been traditionally grown in the southern states and generallyreceive higher market prices.

Rice, Oryza sativa L., is an important and valuable field crop. Thus, acontinuing goal of plant breeders is to develop stable, high yieldingrice cultivars that are agronomically sound. The reasons for this goalare obviously to maximize the amount of grain produced on the land usedand to supply food for both animals and humans. To accomplish this goal,the rice breeder must select and develop rice plants that have thetraits that result in superior cultivars.

The foregoing examples of the related art and limitations relatedtherewith are intended to be illustrative and not exclusive. Otherlimitations of the related art will become apparent to those of skill inthe art upon a reading of the specification.

SUMMARY OF THE INVENTION

The following embodiments and aspects thereof are described inconjunction with systems, tools and methods which are meant to beexemplary and illustrative, not limiting in scope. In variousembodiments, one or more of the above described problems have beenreduced or eliminated, while other embodiments are directed to otherimprovements.

According to the invention, there is provided a novel rice cultivardesignated Calaroma-201. This invention thus relates to the seeds ofrice cultivar Calaroma-201, to the plants of rice Calaroma-201 and tomethods for producing a rice plant produced by crossing the riceCalaroma-201 with itself or another rice line, to methods for producinga rice plant containing in its genetic material one or more transgenesand to the transgenic rice plants produced by that method, and thecreation of variants by mutagenesis or transformation of rice cultivarCalaroma-201. The present invention relates to rice plants havingessentially all of the physiological and morphological characteristicsof rice cultivar Calaroma-201. This invention also relates to methodsfor producing other rice cultivars derived from rice cultivarCalaroma-201 and to the rice cultivar derived by the use of thosemethods. This invention further relates to hybrid rice seeds and plantsproduced by crossing cultivar Calaroma-201 with another rice cultivar.

Thus, any such methods using the rice cultivar Calaroma-201 are part ofthis invention: selfing, backcrosses, hybrid production, crosses topopulations, and the like. All plants produced using rice varietyCalaroma-201 as a parent are within the scope of this invention.Advantageously, the rice variety could be used in crosses with other,different, rice plants to produce first generation (F₁) rice hybridseeds and plants with superior characteristics.

In another aspect, the present invention provides protoplasts andregenerable cells for use in tissue culture of rice plant Calaroma-201.The tissue culture will preferably be capable of regenerating plantshaving the physiological and morphological characteristics of theforegoing rice plant, and of regenerating plants having substantiallythe same genotype as the foregoing rice plant. Preferably, theregenerable cells in such tissue cultures will be embryos, protoplasts,meristematic cells, callus, pollen, leaves, anthers, root tips, flowers,seeds, panicles or stems. Still further, the present invention providesrice plants regenerated from the tissue cultures of the invention.

In another aspect, the present invention provides for single or multiplegene converted plants of Calaroma-201. The single or multipletransferred gene(s) may preferably be a dominant or recessive allele.Preferably, the single or multiple transferred gene(s) will confer suchtraits as herbicide resistance, insect resistance, resistance forbacterial, fungal, or viral disease, male fertility, male sterility,enhanced nutritional quality, and industrial usage. The single ormultiple gene(s) may be a naturally occurring rice gene or a transgeneintroduced through genetic engineering techniques. The invention alsorelates to methods for producing a rice plant containing in its geneticmaterial one or more transgenes and to the transgenic rice plantproduced by that method.

In another aspect, the present invention provides for methods ofintroducing one or more desired trait(s) into the rice line Calaroma-201and plants or seeds obtained from such methods. The desired trait(s) maybe, but not exclusively, a single gene, preferably a dominant but also arecessive allele. Preferably, the transferred gene or genes will confersuch traits as male sterility, herbicide resistance, insect resistance,disease resistance, resistance for bacterial, fungal, or viral disease,male fertility, water stress tolerance, enhanced nutritional quality,modified protein content, enhanced plant quality, enhanced digestibilityand industrial usage. The gene or genes may be naturally occurring ricegene(s). The method for introducing the desired trait(s) may be abackcrossing process making use of a series of backcrosses to the ricecultivar Calaroma-201 during which the desired trait(s) is maintained byselection. The desired trait may also be introduced via transformation.

The invention further relates to methods for genetically modifying arice plant of the rice cultivar Calaroma-201 and to the modified riceplant produced by those methods. The genetic modification methods mayinclude, but are not limited to mutation, genome editing, genesilencing, RNA interference, backcross conversion, genetictransformation, single and multiple gene conversion, and/or direct genetransfer.

The invention further provides methods for developing rice plants in arice plant breeding program using plant breeding techniques includingrecurrent selection, backcrossing, pedigree breeding, restrictionfragment length polymorphism enhanced selection, genetic marker enhancedselection and transformation. Seeds, rice plants, and parts thereof,produced by such breeding methods are also part of the invention.

Still yet another aspect of the invention is a method of producing arice plant derived from the rice cultivar Calaroma-201, the methodcomprising the steps of: (a) preparing a progeny plant derived from ricecultivar Calaroma-201 by crossing a plant of the rice cultivarCalaroma-201 with a second rice plant; and (b) crossing the progenyplant with itself or a second plant to produce a progeny plant of asubsequent generation which is derived from a plant of the rice cultivarCalaroma-201. In one embodiment of the invention, the method furthercomprises: (c) crossing the progeny plant of a subsequent generationwith itself or a second plant; and (d) repeating steps (b) and (c) for,in some embodiments, at least 1, 2, 3, 4 or more additional generationsto produce an inbred rice plant derived from the rice cultivarCalaroma-201. Also provided by the invention is a plant produced by thisand the other methods of the invention.

In another embodiment of the invention, the method of producing a riceplant derived from rice cultivar Calaroma-201 further comprises crossingthe inbred rice plant derived from rice cultivar Calaroma-201 with aplant of a different genotype to produce a seed of a hybrid rice plantderived from rice cultivar Calaroma-201.

In addition to the exemplary aspects and embodiments described above,further aspects and embodiments will become apparent by study of thefollowing descriptions.

DETAILED DESCRIPTION OF THE INVENTION

In the description and tables which follow, a number of terms are used.In order to provide a clear and consistent understanding of thespecification and claims, including the scope to be given such terms,the following definitions are provided:

Abiotic stress. As used herein, abiotic stress relates to all non-livingchemical and physical factors in the environment. Examples of abioticstress include, but are not limited to, drought, flooding, salinity,temperature, and climate change.

Aggregate sheath spot. Is caused by the fungus Rhizoctoniaoryzae-sativae (Sawada) Mordue (=Ceratobasidium oryzae-sativae). Thisdisease causes sheath lesions and can reduce yield and grain quality.California varieties generally rate between 2 and 4 in greenhouse testson a scale of 0 to 4.

Alkali spreading value. Indicator of gelatinization temperature and anindex that measures the extent of disintegration of milled rice kernelin contact with dilute alkali solution. Standard long grains have 3 to 5Alkali Spreading Value (intermediate gelatinization temperature).Standard medium and short grain rice have 6 to 7 Alkali Spreading Values(low gelatinization temperature).

Allele. Allele is any of one or more alternative forms of a gene, all ofwhich alleles relate to one trait or characteristic. In a diploid cellor organism, the two alleles of a given gene occupy corresponding locion a pair of homologous chromosomes.

Alter. The utilization of up-regulation, down-regulation, or genesilencing.

Apparent amylose percent. The most important grain characteristic thatdescribes cooking behavior in each grain class, or type, i.e., long,medium and short grain. The percentage of the endosperm starch of milledrice that is amylose. Standard long grains contain 20 to 23% amylose.Rexmont type long grains contain 24 to 25% amylose. Short and mediumgrain rice contain 16 to 19% amylose. Waxy rice contains 0% amylose.Amylose values will vary over environments.

Backcrossing. Backcrossing is a process in which a breeder repeatedlycrosses hybrid progeny back to one of the parents, for example, a firstgeneration hybrid F₁ with one of the parental genotypes of the F₁hybrid.

Bakanae. Is caused by the fungus Fusarium fujikuroi Nirenberg(=Gibberella fujikuroi). It causes reduced seed germination and abnormalseedling elongation often followed by crown rot. Susceptibility ofvarieties is expressed as percent symptomatic plants.

Blanking %. Visual estimate of the percent of sterile florets (floretsthat are empty with no filled kernels) in the panicle as a measurementof cool temperature induced pollen sterility. Blanking may also beinduced by high temperatures and by genetic incompatibility of theparents. This data may be collected in screening nurseries at coollocations, cool years, and also in screening tests in refrigeratedgreenhouses.

Breakdown. The peak viscosity minus the hot paste viscosity.

Breeding. The genetic manipulation of living organisms.

Cell. Cell as used herein includes a plant cell, whether isolated, intissue culture or incorporated in a plant or plant part.

Cross-pollination. Fertilization by the union of two gametes fromdifferent plants.

Cool paste viscosity. Viscosity measure of rice flour/water slurry afterbeing heated to 95EC and uniformly cooled to 50EC (American Associationof Cereal Chemist). Values less than 200 for cool paste indicate softercooking types of rice.

Days to 50% heading. Average number of days from planting to the daywhen 50% of all panicles are exerted at least partially through the leafsheath. A measure of maturity.

Diploid. A cell or organism having two sets of chromosomes.

Elongation. Cooked kernel elongation is the ratio of the cooked kernellength divided by the uncooked kernel length. Extreme cooked kernelelongation is a unique feature of basmati type rice and an importantquality criterion for that market type.

Embryo. The embryo is the small plant contained within a mature seed.

Essentially all the physiological and morphological characteristics. Aplant having essentially all the physiological and morphologicalcharacteristics means a plant having the physiological and morphologicalcharacteristics of the cultivar that are otherwise present when comparedin the same environment, other than an occasional variant trait thatmight arise during backcrossing, direct introduction of a transgene orgenetic modification.

F_(#). The “F” symbol denotes the filial generation, and the # is thegeneration number, such as F₁, F₂, F₃, etc.

Final viscosity. Viscosity at the end of the test or cold paste.

Gene. As used herein, “gene” refers to a unit of inheritancecorresponding to DNA or RNA that code for a type of protein or for anRNA chain that has a function in the organism.

Gene silencing. The interruption or suppression of the expression of agene at the level of transcription or translation.

Genetically modified. Describes an organism that has received geneticmaterial from another organism, or had its genetic material modified,resulting in a change in one or more of its phenotypic characteristics.Methods used to modify, introduce or delete the genetic material mayinclude mutation breeding, genome editing, RNA interference, genesilencing, backcross conversion, genetic transformation, single andmultiple gene conversion, and/or direct gene transfer.

Genome editing. A type of genetic engineering in which DNA is inserted,replaced, modified or removed from a genome using artificiallyengineered nucleases or other targeted changes using homologousrecombination. Examples include but are not limited to use of zincfinger nucleases (ZFNs), TAL effector nucleases (TALENs), meganucleases,CRISPR/Cas9, and other CRISPR related technologies. (Ma et. al.,Molecular Plant, 9:961-974 (2016); Belhaj et. al., Current Opinion inBiotechnology, 32:76-84 (2015)).

Genotype. Refers to the genetic constitution of a cell or organism.

Grain length (L). Length of a rice grain is measured in millimeters.

Grain width (W). Width of a rice grain is measured in millimeters.

Grain yield. Grain yield is measured in pounds per acre and at 14.0%moisture. Grain yield of rice is determined by the number of paniclesper unit area, the number of fertile florets per panicle, and grainweight per floret.

Haploid. A cell or organism having one set of the two sets ofchromosomes in a diploid.

Harvest moisture. The percent of moisture of the grain when harvested.

Head rice. Unbroken kernels of milled rice.

Hot paste viscosity. Viscosity measure of rice flour/water slurry afterbeing heated to 95EC. Lower values indicate softer and stickier cookingtypes of rice.

Length/Width (L/W) ratio. This ratio is determined by dividing theaverage length (L) by the average width (W).

Linkage. Refers to a phenomenon wherein alleles on the same chromosometend to segregate together more often than expected by chance if theirtransmission was independent.

Linkage disequilibrium. Refers to a phenomenon wherein alleles tend toremain together in linkage groups when segregating from parents tooffspring, with a greater frequency than expected from their individualfrequencies.

Locus. A defined segment of DNA. A locus confers one or more traits suchas, for example, male sterility, herbicide resistance trait, insectresistance, disease resistance, and improved yield. The trait may be,for example, conferred by a naturally occurring gene introduced into thegenome of the variety by backcrossing, a natural or induced mutation, ora transgene introduced through genetic transformation techniques. Alocus may comprise one or more alleles integrated at a singlechromosomal location.

Lodging resistance (also called Straw strength). Lodging is measured asa subjective rating and is percentage of the plant stems leaning orfallen completely to the ground before harvest. Visual scoring where0%=all plants standing to 100%=all plant in plot are laying flat on thesoil surface. Lodged plants are difficult to harvest and reduce yieldand grain quality.

Milling yield. Milling yield is the total amount of milled rice (wholeand broken kernels) recovered after removal of hulls, bran, and germ bymilling and head-rice yield, the total amount of whole kernels recoveredafter milling. Values are expressed as weight percentage of the originalpaddy or rough rice sample that was milled. For example, a milling yieldof 65/70 is a sample of 100 grams of rough rice that produced 65 gramsof head rice and 70 grams of total milled rice.

Multiple Gene Converted (Conversion). Multiple gene converted(conversion) includes plants developed by a plant breeding techniquecalled backcrossing wherein essentially all of the desired morphologicaland physiological characteristics of a variety are recovered, whileretaining two or more genes transferred into the variety via crossingand backcrossing. The term can also refer to the introduction ofmultiple genes through genetic engineering techniques known in the art.

Nucleic acid. An acidic, chainlike biological macromolecule consistingof multiple repeat units of phosphoric acid, sugar and purine andpyrimidine bases.

Nutraceutical. Refers to a food or food product that provides health andor medical benefits, including the prevention and treatment of disease.Such products may range from isolated nutrients, dietary supplements andspecific diets to genetically engineered foods, herbal products, andprocessed foods such as cereals, soups and beverages.

1000 Grain wt. The weight of 1000 rice grains as measured in grams. Itcan be for paddy, brown or milled rice.

Pedigree. Refers to the lineage or genealogical descent of a plant.

Pedigree distance. Relationship among generations based on theirancestral links as evidenced in pedigrees. May be measured by thedistance of the pedigree from a given starting point in the ancestry.

Percent identity. Percent identity as used herein refers to thecomparison of the homozygous alleles of two rice varieties. Percentidentity is determined by comparing a statistically significant numberof the homozygous alleles of two developed varieties. For example, apercent identity of 90% between rice variety 1 and rice variety 2 meansthat the two varieties have the same allele at 90% of their loci.

Peak viscosity. The maximum viscosity attained during heating when astandardized instrument-specific protocol is applied to a defined riceflour-water slurry.

Plant. As used herein, the term “plant” includes reference to animmature or mature whole plant, including a plant from which seed,grain, or anthers have been removed. Seed or embryo that will producethe plant is also considered to be the plant.

Plant height. Plant height measured in centimeters or inches is takenfrom soil surface to the tip of the extended panicle at harvest.

Plant parts. As used herein, the term “plant parts” (or a rice plant, ora part thereof) includes but is not limited to protoplasts, leaves,stems, roots, root tips, anthers, pistils, seed, grain, embryo, pollen,ovules, cotyledon, hypocotyl, pod, flower, shoot, tissue, petiole,cells, meristematic cells, and the like.

Progeny. As used herein, includes an F₁ rice plant produced from thecross of two rice plants where at least one plant includes rice cultivarCalaroma-201 and progeny further includes, but is not limited to,subsequent F₂, F₃, F₄, F₅, F₆, F₇, F₈, F₉, and F₁₀ generational crosseswith the recurrent parental line.

Quantitative Trait Loci (QTL). Quantitative trait loci (QTL) refer togenetic loci that control to some degree numerically representabletraits that are usually continuously distributed.

RVA viscosity. Rapid Visco Analyzer is a widely used laboratoryinstrument to examine paste viscosity, or thickening ability of milledrice during the cooking process.

RVU. The RVA scale is measured in RVUs. This is the native viscosityunit of the RVA. 1 RVU is equivalent to 12 CP. CP equals “centipoises”which equals unit of viscosity (kg s^(−l)m⁻¹) and 1 kg s⁻¹ m⁻¹ equals1000 centipoises.

Regeneration. Regeneration refers to the development of a plant fromtissue culture.

Seedling Vigor. Seedling vigor refers to the ability of the seedling toemerge rapidly through the soil or water after planting. It isfrequently measured by visual observation field test and assigned arelative score.

Setback. Setback 1 is the final viscosity minus trough viscosity.Setback 2 is the final viscosity minus peak viscosity and is what ismost commonly referred to for rice quality testing.

Single gene converted (Conversion). Single gene converted (conversion),also known as coisogenic plants, refers to plants which are developed bya plant breeding technique called backcrossing wherein essentially allof the desired morphological and physiological characteristics of avariety are recovered in addition to the single gene transferred intothe variety via the backcrossing technique or via genetic engineering.

Stem rot. Is caused by the fungus Sclerotium oryzae Cattaneo(=Magnaporthe salvinii). It produces sheath and stem lesions that canreduce yield and grain quality. California varieties are generally ratedbetween 4.5 and 7.5 on a scale of 0 to 10.

Texture score. A relative subjective score used by the breeder inevaluating cooked rice samples. A score of 4 being most sticky and ascore of 2 being the least sticky.

Trough viscosity. The minimum viscosity after the peak, normallyoccurring when the sample starts to cool.

Rice cultivar Calaroma-201, an early maturing Jasmine-type aromatic longgrain rice, was developed at the California Cooperative Rice ResearchFoundation (CCRRF), Inc., Rice Experiment Station (RES), at Biggs,Calif. from a cross designated R400709 made in the spring of 2009. Thepedigree of Calaroma-201 is as follows: R40709=07Y603/JES; where07Y603=02Y710/99Y529; 02Y710=00KDMX3-3; 99Y529=90Y563/3/L-202/QC//L-202.The official pedigree designation for Calaroma-201 is“OOKDMX3-3/4/90Y563/3/L-202/QUIZHAW/L-202/5/JES”. L-202 is an earlymaturing California long grain variety released by RES in 1984 and is nolonger in commercial production. 90Y563 is an advanced line from theLong Grains Project at RES. Quizhaw is a high yielding rice introductionthat came from China. OOKDMX3-3 is photoperiod-insensitive mutant linederived from a Thai Jasmine variety Khao Dawk Mali (KDM) developed atRES. JES is a mutant of KDM released by the USDA-ARS and University ofArkansas.

Rice cultivar Calaroma-201 was developed using the pedigree selectionmethod and underwent 11 years of selection and evaluation from theoriginal cross until the production of its foundation seed.

Rice cultivar Calaroma-201 is a long-grain rice (aromatic market type)that can be classified as Gramineae, Oryza sativa L., and a tropicaljaponica. Calaroma-201 is a photoperiod insensitive, early maturing,semi-dwarf cultivar. The floret hull (lemma and palea), the hulls andleaves are of intermediate pubescence. Rice cultivar Calaroma-201 is thefirst jasmine class to be proposed for release by RES to the Californiarice industry.

Calaroma-201 was tested under the experimental designation of 15Y84 inthe University of California Cooperative Extension (UCCE) Statewide (SW)Yield Tests from 2015-2017 in a total of 22 experiments. Testingcomparisons were made to L-206 and A-202, California long grainvarieties in commercial production.

Rice cultivar Calaroma-201 grain yield across 22 experiments in the SWtest averaged 9,450 lbs./acre compared to 9,310 and 8,890 lbs./acre forL-206 and A-202, respectively, with overall 3-year yield advantage of6.3% and 1.5% over A-202 and L-206, respectively.

Rice cultivar Calaroma-201 is comparable to L-206 and A-202 in terms ofoverall seedling vigor score and lodging scores. In comparisons withother California long grain varieties, the days to 50% heading ofCalaroma-201 was about 5 days later than L-206 and 1 day later thanA-202. Calaroma-201 was slightly taller than L-206, but shorter thanA-202 by about 8 cm.

The area of adaptation in California of Calaroma-201 is similar toL-206, but as with other RES-bred long grains, it is not recommended incolder rice areas.

Rice cultivar Calaroma-201 has shown uniformity and stability asdescribed in the following variety description information. It has beenself-pollinated a sufficient number of generations with carefulattention to uniformity of plant type. The line has been increased withcontinued observation for uniformity. Initial headrow purification wasinitiated in the RES greenhouse in the winter of 2015-2016. Headrowswere again planted in the field in 2016 and 2017, where Calaroma-201 wasdeemed distinct, uniform and stable. Additional tests on purity andfingerprinting using DNA markers were used for seed purification. The2017 foundation seed field of passed field inspection for certificationby the California Crop Improvement Association.

Rice cultivar Calaroma-201 has the following morphologic and othercharacteristics (based primarily on data collected in California).

Table 1 Variety Description Information

Grain type: Long

Days to maturity (50% heading): 86

Culm:

-   -   Angle (degrees from perpendicular after flowering): Erect (less        than 30°)    -   Length (soil level to top of extended panicle on main stem):        91.0 cm    -   Height class: Short    -   Internode color (after flowering): Green    -   Strength (lodging resistance): 2 (most plants not lodged)

Flag leaf (at maturity):

-   -   Length: 22.1 cm    -   Width: 1.6 cm    -   Pubescence: Intermediate    -   Leaf angle (after heading): Erect    -   Blade color (at heading): Dark green    -   Basal leaf sheath color (at heading): Green

Ligule:

-   -   Length (from base of collar to the tip, at late vegetative        stage): 6.0 mm    -   Color (late vegetative stage): White    -   Shape: Acute to acuminate    -   Collar Color (late vegetative stage): Pale green    -   Auricle Color (late vegetative stage): Pale green

Panicle:

-   -   Length: 18.3 cm    -   Type: Intermediate    -   Secondary branching: Light    -   Exertion (near maturity): 100% exerted    -   Shattering (at maturity): Low (less than 5%)    -   Threshability: Easy

Grain (spikelet):

-   -   Awns (after full heading): Absent    -   Apiculus color (at maturity): Straw    -   Apiculus color (after full heading): Purple    -   Stigma color: White    -   Lemma and palea color (at maturity): Straw    -   Lemma and palea pubescence: Short hairs    -   Spikelet sterility (at maturity): Highly fertile (>90%)

Grain (seed):

-   -   Seed coat color: Light brown    -   Endosperm type: Nonglutinous (nonwaxy)    -   Endosperm translucency: Clear    -   Endosperm chalkiness: Small (less than 10% of sample)    -   Scent: Scented    -   Shape class (length/width ratio):        -   Paddy: Long (3.4:1 and more)            -   Length: 9.93 mm            -   Width: 2.40 mm            -   L/W ratio: 4.14            -   1000 Grains: 27.29 g        -   Brown: Long (3.1:1 and more)            -   Length: 7.98 mm            -   Width: 2.14 mm            -   L/W ratio: 3.73            -   1000 Grains: 22.81 g        -   Milled: Long (3.0:1 and more)            -   Length: 7.27 mm            -   Width: 2.04 mm            -   L/W ratio: 1.68            -   1000 Grains: 19.72 g    -   Milling quality (% hulls): 21    -   Milling yield (% whole kernel (head) rice to rough rice): 60%    -   Protein (brown): 5.8%    -   Amylose: 15.8    -   Alkali spreading value: 7        -   Gelatinization temperature type: Low        -   Amylographic paste viscosity (RVA measured in RVU):            -   Peak: 274            -   Hot paste: 128            -   Cooled paste: 231            -   Setback: −43

Resistance to low temperature:

-   -   Germination and seedling vigor: High    -   Flowering (spikelet fertility): Medium

Seedling vigor not related to low temperature: High

Disease resistance:

-   -   Rice blast (Pyricularia oryzae): Susceptible to races in        California    -   Aggregate sheath spot (Rhizoctonia oryzae-sativae): Moderately        susceptible    -   Stem rot (Sclerotium oryzae): Moderately susceptible

Insect resistance: None

This invention also is directed to methods for producing a rice plant bycrossing a first parent rice plant with a second parent rice plantwherein either the first or second parent rice plant is a rice plant ofthe line Calaroma-201. Further, both first and second parent rice plantscan come from the rice cultivar Calaroma-201. Still further, thisinvention also is directed to methods for producing a rice cultivarCalaroma-201-derived rice plant by crossing rice cultivar Calaroma-201with a second rice plant and growing the progeny seed, and repeating thecrossing and growing steps with the rice cultivar Calaroma-201-derivedplant from 0 to 7 times. Thus, any such methods using the rice cultivarCalaroma-201 are part of this invention: selfing, backcrosses, hybridproduction, crosses to populations, and the like. All plants producedusing rice cultivar Calaroma-201 as a parent are within the scope ofthis invention, including plants derived from rice cultivarCalaroma-201. Advantageously, the rice cultivar is used in crosses withother, different, rice cultivars to produce first generation (F₁) riceseeds and plants with superior characteristics.

It should be understood that the cultivar can, through routinemanipulation of cytoplasmic or other factors, be produced in amale-sterile form. Such embodiments are also contemplated within thescope of the present claims.

As used herein, the term plant includes plant cells, plant protoplasts,plant cell tissue cultures from which rice plants can be regenerated,plant calli, plant clumps and plant cells that are intact in plants orparts of plants, such as embryos, pollen, ovules, flowers, glumes,panicles, leaves, stems, roots, root tips, anthers, pistils and thelike.

Further Embodiments of the Invention

Rice in general is an important and valuable vegetable crop. Thus, acontinuing goal of rice plant breeders is to develop stable, highyielding rice cultivars that are agronomically sound. To accomplish thisgoal, the rice breeder must select and develop rice plants with traitsthat result in superior cultivars.

Plant breeding techniques known in the art and used in a rice plantbreeding program include, but are not limited to, pedigree breeding,recurrent selection, mass selection, single or multiple-seed descent,bulk selection, backcrossing, open pollination breeding, restrictionfragment length polymorphism enhanced selection, genetic marker enhancedselection, making double haploids, and transformation. Oftencombinations of these techniques are used. The development of ricevarieties in a plant breeding program requires, in general, thedevelopment and evaluation of homozygous varieties. There are manyanalytical methods available to evaluate a new variety. The oldest andmost traditional method of analysis is the observation of phenotypictraits, but genotypic analysis may also be used.

Using Rice Cultivar Calaroma-201 to Develop Other Rice Varieties

This invention also is directed to methods for producing a rice plant bycrossing a first parent rice plant with a second parent rice plantwherein the first or second parent rice plant is a rice plant ofcultivar Calaroma-201. Further, both first and second parent rice plantscan come from rice cultivar Calaroma-201. Also provided are methods forproducing a rice plant having substantially all of the morphological andphysiological characteristics of cultivar Calaroma-201, by crossing afirst parent rice plant with a second parent rice plant wherein thefirst and/or the second parent rice plant is a plant havingsubstantially all of the morphological and physiological characteristicsof cultivar Calaroma-201 set forth in Table 1, as determined at the 5%significance level when grown in the same environmental conditions. Theother parent may be any rice plant, such as a rice plant that is part ofa synthetic or natural population. Thus, any such methods using ricecultivar Calaroma-201 are part of this invention: selfing, backcrosses,hybrid production, crosses to populations, and the like. All plantsproduced using rice cultivar Calaroma-201 as at least one parent arewithin the scope of this invention, including those developed fromcultivars derived from rice cultivar Calaroma-201.

The cultivar of the invention can also be used for transformation whereexogenous genes are introduced and expressed by the cultivar of theinvention. Genetic variants created either through traditional breedingmethods using rice cultivar Calaroma-201 or through transformation ofcultivar Calaroma-201 by any of a number of protocols known to those ofskill in the art are intended to be within the scope of this invention.

The following describes breeding methods that may be used with ricecultivar Calaroma-201 in the development of further rice plants. Onesuch embodiment is a method for developing a progeny rice plant in arice plant breeding program comprising: obtaining the rice plant, or apart thereof, of cultivar Calaroma-201, utilizing said plant or plantpart as a source of breeding material, and selecting a rice cultivarCalaroma-201 progeny plant with molecular markers in common withcultivar Calaroma-201 and/or with morphological and/or physiologicalcharacteristics selected from the characteristics listed in Table 1.Breeding steps that may be used in the rice plant breeding programinclude, but are not limited to, pedigree breeding, backcrossing,mutation breeding, and recurrent selection. In conjunction with thesesteps, techniques such as RFLP-enhanced selection, genetic markerenhanced selection (for example SSR markers) and the making of doublehaploids may be utilized.

Another method involves producing a population of rice cultivarCalaroma-201 progeny rice plants, comprising crossing cultivarCalaroma-201 with another rice plant, thereby producing a population ofrice plants, which, on average, derive 50% of their alleles from ricecultivar Calaroma-201. A plant of this population may be selected andrepeatedly selfed or sibbed with a rice cultivar resulting from thesesuccessive filial generations. One embodiment of this invention is therice cultivar produced by this method and that has obtained at least 50%of its alleles from rice cultivar Calaroma-201.

Progeny of rice cultivar Calaroma-201 may also be characterized throughtheir filial relationship with rice cultivar Calaroma-201, as forexample, being within a certain number of breeding crosses of ricecultivar Calaroma-201. A breeding cross is a cross made to introduce newgenetics into the progeny, and is distinguished from a cross, such as aself or a sib cross, made to select among existing genetic alleles. Thelower the number of breeding crosses in the pedigree, the closer therelationship between rice cultivar Calaroma-201 and its progeny. Forexample, progeny produced by the methods described herein may be within1, 2, 3, 4 or 5 breeding crosses of rice cultivar Calaroma-201.

One of ordinary skill in the art of plant breeding would know how toevaluate the traits of two plant varieties to determine if there is nosignificant difference between the two traits expressed by thosevarieties. For example, see, Fehr and Walt, Principles of CultivarDevelopment, pp. 261-286 (1987). Thus the invention includes ricecultivar Calaroma-201 progeny rice plants comprising a combination of atleast two cultivar Calaroma-201 traits selected from the groupconsisting of those listed in Table 1 or the cultivar Calaroma-201combination of traits listed in the Detailed Description of theInvention, so that said progeny rice plant is not significantlydifferent for said traits than rice cultivar Calaroma-201 as determinedat the 5% significance level when grown in the same environmentalconditions. Using techniques described herein, molecular markers may beused to identify said progeny plant as a rice cultivar Calaroma-201progeny plant. Mean trait values may be used to determine whether traitdifferences are significant, and preferably the traits are measured onplants grown under the same environmental conditions. Once such avariety is developed its value is substantial since it is important toadvance the germplasm base as a whole in order to maintain or improvetraits such as yield, disease resistance, pest resistance, and plantperformance in extreme environmental conditions.

The goal of rice plant breeding is to develop new, unique, and superiorrice cultivars. The breeder initially selects and crosses two or moreparental lines, followed by repeated selfing and selection, producingmany new genetic combinations. The breeder can theoretically generatebillions of different genetic combinations via crossing, selfing, andmutations. The breeder has no direct control at the cellular level andthe cultivars that are developed are unpredictable. Thisunpredictability is because the breeder's selection occurs in uniqueenvironments, with no control at the DNA level (using conventionalbreeding procedures), and with millions of different possible geneticcombinations being generated. A breeder of ordinary skill in the artcannot predict the final resulting lines he develops, except possibly ina very gross and general fashion. The same breeder cannot produce thesame line twice by using the exact same original parents and the sameselection techniques. Therefore, two breeders will never develop thesame line, or even very similar lines, having the same rice traits.

Pedigree breeding is used commonly for the improvement ofself-pollinating crops or inbred lines of cross-pollinating crops.Pedigree breeding starts with the crossing of two genotypes, such asrice cultivar Calaroma-201 or a rice variety having all of themorphological and physiological characteristics of Calaroma-201, andanother rice variety having one or more desirable characteristics thatis lacking or which complements rice cultivar Calaroma-201. If the twooriginal parents do not provide all the desired characteristics, othersources can be included in the breeding population. In the pedigreemethod, superior plants are selfed and selected in successive filialgenerations. In the succeeding filial generations, the heterozygouscondition gives way to the homozygous allele condition as a result ofinbreeding. Typically in the pedigree method of breeding, five or moresuccessive filial generations of selfing and selection is practiced: F₁to F₂; F₂ to F₃; F₃ to F₄; F₄ to F₅; etc. In some examples, 1, 2, 3, 4,5, 6, 7, 8, 9, 10, or more generations of selfing and selection arepracticed. After a sufficient amount of inbreeding, successive filialgenerations will serve to increase seed of the developed variety.Preferably, the developed variety comprises homozygous alleles at about95% or more of its loci.

In addition to being used to create backcross conversion populations,backcrossing can also be used in combination with pedigree breeding. Asdiscussed previously, backcrossing can be used to transfer one or morespecifically desirable traits from one variety (the donor parent) to adeveloped variety (the recurrent parent), which has good overallagronomic characteristics yet may lack one or more other desirabletraits. However, the same procedure can be used to move the progenytoward the genotype of the recurrent parent but at the same time retainmany components of the non-recurrent parent by stopping the backcrossingat an early stage and proceeding with selfing and selection. Forexample, a rice variety may be crossed with another variety to produce afirst generation progeny plant. The first generation progeny plant maythen be backcrossed to one of its parent varieties to create a F₁BC₁.Progeny are selfed and selected so that the newly developed variety hasmany of the attributes of the recurrent parent and yet several of thedesired attributes of the donor parent. This approach leverages thevalue and strengths of both parents for use in new rice varieties.

Therefore, in some examples a method of making a backcross conversion ofrice cultivar Calaroma-201, comprising the steps of crossing a plant ofrice cultivar Calaroma-201 or a rice variety having all of themorphological and physiological characteristics of Calaroma-201 with adonor plant possessing a desired trait to introduce the desired trait,selecting an F₁ progeny plant containing the desired trait, andbackcrossing the selected F₁ progeny plant to a plant of rice cultivarCalaroma-201 are provided. This method may further comprise the step ofobtaining a molecular marker profile of rice cultivar Calaroma-201 andusing the molecular marker profile to select for a progeny plant withthe desired trait and the molecular marker profile of Calaroma-201. Themolecular marker profile can comprise information from one or moremarkers. In one example the desired trait is a mutant gene or transgenepresent in the donor parent. In another example, the desired trait is anative trait in the donor parent.

Mass and recurrent selections can be used to improve populations ofeither self- or cross-pollinating crops. A genetically variablepopulation of heterozygous individuals is either identified or createdby intercrossing several different parents. The best plants are selectedbased on individual superiority, outstanding progeny, or excellentcombining ability. The selected plants are intercrossed to produce a newpopulation in which further cycles of selection are continued.

The single-seed descent procedure in the strict sense refers to plantinga segregating population, harvesting a sample of one seed per plant, andusing the one-seed sample to plant the next generation. When thepopulation has been advanced from the F₂ to the desired level ofinbreeding, the plants from which lines are derived will each trace todifferent F₂ individuals. The number of plants in a population declineseach generation due to failure of some seeds to germinate or some plantsto produce at least one seed. As a result, not all of the F₂ plantsoriginally sampled in the population, will be represented by a progenywhen generation advance is completed.

Mutation breeding is another method of introducing new traits into ricevarieties. Mutations that occur spontaneously or are artificiallyinduced can be useful sources of variability for a plant breeder. Thegoal of artificial mutagenesis is to increase the rate of mutation for adesired characteristic. Mutation rates can be increased by manydifferent means including temperature, long-term seed storage, tissueculture conditions, radiation (such as X-rays, Gamma rays, neutrons,Beta radiation, or ultraviolet radiation), chemical mutagens (such asbase analogs like 5-bromo-uracil), antibiotics, alkylating agents (suchas sulfur mustards, nitrogen mustards, epoxides, ethyleneamines,sulfates, sulfonates, sulfones, or lactones), azide, hydroxylamine,nitrous acid or acridines. Once a desired trait is observed throughmutagenesis the trait may then be incorporated into existing germplasmby traditional breeding techniques. Details of mutation breeding can befound in “Principles of Cultivar Development” by Fehr, MacmillanPublishing Company, 1993. In addition, mutations created in other riceplants may be used to produce a backcross conversion of rice cultivarCalaroma-201 that comprises such mutation.

Selection of rice plants for breeding is not necessarily dependent onthe phenotype of a plant and instead can be based on geneticinvestigations. For example, one may utilize a suitable genetic markerwhich is closely associated with a trait of interest. One of thesemarkers may therefore be used to identify the presence or absence of atrait in the offspring of a particular cross, and hence may be used inselection of progeny for continued breeding. This technique may commonlybe referred to as marker assisted selection. Any other type of geneticmarker or other assay which is able to identify the relative presence orabsence of a trait of interest in a plant may also be useful forbreeding purposes. Procedures for marker assisted selection applicableto the breeding of rice are well known in the art. Such methods will beof particular utility in the case of recessive traits and variablephenotypes, or where conventional assays may be more expensive, timeconsuming or otherwise disadvantageous. Types of genetic markers whichcould be used in accordance with the invention include, but are notnecessarily limited to, Isozyme Electrophoresis, Restriction FragmentLength Polymorphisms (RFLPs), Simple Sequence Length Polymorphisms(SSLPs) (Williams et al., Nucleic Acids Res., 18:6531-6535, 1990),Randomly Amplified Polymorphic DNAs (RAPDs), DNA AmplificationFingerprinting (DAF), Sequence Characterized Amplified Regions (SCARs),Arbitrary Primed Polymerase Chain Reaction (AP-PCR), Amplified FragmentLength Polymorphisms (AFLPs) (EP 534 858, specifically incorporatedherein by reference in its entirety), Simple Sequence Repeats (SSRs),and Single Nucleotide Polymorphisms (SNPs) (Wang et al., Science,280:1077-1082, 1998).

The production of double haploids can also be used for the developmentof homozygous varieties in a breeding program. Double haploids areproduced by the doubling of a set of chromosomes from a heterozygousplant to produce a completely homozygous individual. For example, see,Wan, et al., “Efficient Production of Doubled Haploid Plants ThroughColchicine Treatment of Anther-Derived Maize Callus,” Theoretical andApplied Genetics, 77:889-892 (1989) and U.S. Pat. No. 7,135,615. Thiscan be advantageous because the process omits the generations of selfingneeded to obtain a homozygous plant from a heterozygous source.

Descriptions of other breeding methods that are commonly used fordifferent traits and crops can be found in one of several referencebooks (e.g., Allard, “Principles of plant breeding,” John Wiley & Sons,NY, University of California, Davis, Calif., 50-98, 1960; Simmonds,“Principles of crop improvement,” Longman, Inc., NY, 369-399, 1979;Sneep and Hendriksen, “Plant breeding perspectives,” Wageningen (ed),Center for Agricultural Publishing and Documentation, 1979; Fehr, In:Soybeans: Improvement, Production and Uses,” 2d Ed., Manograph 16:249,1987; Fehr, “Principles of cultivar development,” Theory and Technique(Vol 1) and Crop Species Soybean (Vol 2), Iowa State Univ., MacmillianPub. Co., NY, 360-376, 1987; Poehlman and Sleper, “Breeding Field Crops”Iowa State University Press, Ames, 1995; Sprague and Dudley, eds., Cornand Improvement, 5th ed., 2006).

Genotypic Profile of Calaroma-201 and Progeny

In addition to phenotypic observations, a plant can also be identifiedby its genotype. The genotype of a plant can be characterized through agenetic marker profile which can identify plants of the same variety ora related variety, or which can be used to determine or validate apedigree. Genetic marker profiles can be obtained by techniques such asrestriction fragment length polymorphisms (RFLPs), randomly amplifiedpolymorphic DNAs (RAPDs), arbitrarily primed polymerase chain reaction(AP-PCR), DNA amplification fingerprinting (DAF), sequence characterizedamplified regions (SCARs), amplified fragment length polymorphisms(AFLPs), simple sequence repeats (SSRs) also referred to asmicrosatellites, single nucleotide polymorphisms (SNPs), or genome-wideevaluations such as genotyping-by-sequencing (GBS). For example, seeCregan et al. (1999) “An Integrated Genetic Linkage Map of the SoybeanGenome” Crop Science 39:1464-1490, and Berry et al. (2003) “AssessingProbability of Ancestry Using Simple Sequence Repeat Profiles:Applications to Maize Inbred Lines and Soybean Varieties” Genetics165:331-342, each of which are incorporated by reference herein in theirentirety. Favorable genotypes and or marker profiles, optionallyassociated with a trait of interest, may be identified by one or moremethodologies.

In some examples one or more markers are used, including but not limitedto AFLPs, RFLPs, ASH, SSRs, SNPs, indels, padlock probes, molecularinversion probes, microarrays, sequencing, and the like. In somemethods, a target nucleic acid is amplified prior to hybridization witha probe. In other cases, the target nucleic acid is not amplified priorto hybridization, such as methods using molecular inversion probes (see,for example Hardenbol et al. (2003) Nat Biotech 21:673-678). In someexamples, the genotype related to a specific trait is monitored, whilein other examples, a genome-wide evaluation including but not limited toone or more of marker panels, library screens, association studies,microarrays, gene chips, expression studies, or sequencing such aswhole-genome resequencing and genotyping-by-sequencing (GB S) may beused. In some examples, no target-specific probe is needed, for exampleby using sequencing technologies, including but not limited tonext-generation sequencing methods (see, for example, Metzker (2010) NatRev Genet 11:31-46; and, Egan et al. (2012) Am J Bot 99:175-185) such assequencing by synthesis (e.g., Roche 454 pyrosequencing, Illumina GenomeAnalyzer, and Ion Torrent PGM or Proton systems), sequencing by ligation(e.g., SOLiD from Applied Biosystems, and Polnator system from AzcoBiotech), and single molecule sequencing (SMS or third-generationsequencing) which eliminate template amplification (e.g., Helicossystem, and PacBio RS system from Pacific BioSciences). Furthertechnologies include optical sequencing systems (e.g., Starlight fromLife Technologies), and nanopore sequencing (e.g., GridION from OxfordNanopore Technologies). Each of these may be coupled with one or moreenrichment strategies for organellar or nuclear genomes in order toreduce the complexity of the genome under investigation via PCR,hybridization, restriction enzyme (see, e.g., Elshire et al. (2011) PLoSONE 6:e19379), and expression methods. In some examples, no referencegenome sequence is needed in order to complete the analysis.

The invention further provides a method of determining the genotype of aplant of rice cultivar Calaroma-201, or a first generation progenythereof, which may comprise obtaining a sample of nucleic acids fromsaid plant and detecting in said nucleic acids a plurality ofpolymorphisms. This method may additionally comprise the step of storingthe results of detecting the plurality of polymorphisms on a computerreadable medium. The plurality of polymorphisms are indicative of and/orgive rise to the expression of the morphological and physiologicalcharacteristics of rice cultivar Calaroma-201.

With any of the genotyping techniques mentioned herein, polymorphismsmay be detected when the genotype and/or sequence of the plant ofinterest is compared to the genotype and/or sequence of one or morereference plants. The polymorphism revealed by these techniques may beused to establish links between genotype and phenotype. Thepolymorphisms may thus be used to predict or identify certain phenotypiccharacteristics, individuals, or even species. The polymorphisms aregenerally called markers. It is common practice for the skilled artisanto apply molecular DNA techniques for generating polymorphisms andcreating markers. The polymorphisms of this invention may be provided ina variety of mediums to facilitate use, e.g. a database or computerreadable medium, which may also contain descriptive annotations in aform that allows a skilled artisan to examine or query the polymorphismsand obtain useful information.

In some examples, a plant, a plant part, or a seed of rice cultivarCalaroma-201 may be characterized by producing a molecular profile. Amolecular profile may include, but is not limited to, one or moregenotypic and/or phenotypic profile(s). A genotypic profile may include,but is not limited to, a marker profile, such as a genetic map, alinkage map, a trait maker profile, a SNP profile, an SSR profile, agenome-wide marker profile, a haplotype, and the like. A molecularprofile may also be a nucleic acid sequence profile, and/or a physicalmap. A phenotypic profile may include, but is not limited to, a proteinexpression profile, a metabolic profile, an mRNA expression profile, andthe like.

SSR technology is currently the most efficient and practical markertechnology; more marker loci can be routinely used and more alleles permarker locus can be found using SSRs in comparison to RFLPs. Forexample, Diwan and Cregan described a highly polymorphic microsatellitelocus in soybean with as many as 26 alleles. Diwan, N. and Cregan, P.B., Theor. Appl. Genet., 95:22-225 (1997). SNPs may also be used toidentify the unique genetic composition of the invention and progenyvarieties retaining that unique genetic composition. Various molecularmarker techniques may be used in combination to enhance overallresolution.

Molecular markers, which include markers identified through the use oftechniques such as Isozyme Electrophoresis, RFLPs, RAPDs, AP-PCR, DAF,SCARs, AFLPs, SSRs, and SNPs, may be used in plant breeding. One use ofmolecular markers is Quantitative Trait Loci (QTL) mapping. QTL mappingis the use of markers which are known to be closely linked to allelesthat have measurable effects on a quantitative trait. Selection in thebreeding process is based upon the accumulation of markers linked to thepositive effecting alleles and/or the elimination of the markers linkedto the negative effecting alleles from the plant's genome.

Molecular markers can also be used during the breeding process for theselection of qualitative traits. For example, markers closely linked toalleles or markers containing sequences within the actual alleles ofinterest can be used to select plants that contain the alleles ofinterest during a backcrossing breeding program. The markers can also beused to select toward the genome of the recurrent parent and against themarkers of the donor parent. This procedure attempts to minimize theamount of genome from the donor parent that remains in the selectedplants. It can also be used to reduce the number of crosses back to therecurrent parent needed in a backcrossing program. The use of molecularmarkers in the selection process is often called genetic marker enhancedselection or marker-assisted selection. Molecular markers may also beused to identify and exclude certain sources of germplasm as parentalvarieties or ancestors of a plant by providing a means of trackinggenetic profiles through crosses.

Particular markers used for these purposes are not limited to the set ofmarkers disclosed herein, but may include any type of marker and markerprofile which provides a means of distinguishing varieties. In additionto being used for identification of rice cultivar Calaroma-201, a hybridproduced through the use of Calaroma-201, and the identification orverification of pedigree for progeny plants produced through the use ofCalaroma-201, a genetic marker profile is also useful in developing agene conversion of Calaroma-201.

Rice DNA molecular marker linkage maps have been rapidly constructed andwidely implemented in genetic studies such as in Zhu, J. H., et al.(1999) “Toward rice genome scanning by map-based AFLP fingerprinting”Mol. Gene Genetics. 261(1):184-195; Cheng, Z., et al (2001) “Toward acytological characterization of the rice genome” Genome Research.11(12):2133-2141; Ahn, S., et al. (1993) “Comparative linkage maps ofthe rice and maize genomes” Proc. Natl. Acad. Sci. USA.90(17):7980-7984; and Kao, F. I., et al. (2006) “An integrated map ofOryza sativa L. chromosome 5” Theor. Appl. Genet. 112(5):891-902.Sequences and PCR conditions of SSR Loci in rice as well as the mostcurrent genetic map may be found in RiceBLAST and the TIGR Rice GenomeAnnotation on the World Wide Web.

Means of performing genetic marker profiles using SNP and SSRpolymorphisms are well known in the art. SNPs are genetic markers basedon a polymorphism in a single nucleotide. A marker system based on SNPscan be highly informative in linkage analysis relative to other markersystems in that multiple alleles may be present.

The SSR profile of rice cultivar Calaroma-201 can be used to identifyplants comprising rice cultivar Calaroma-201 as a parent, since suchplants will comprise the same homozygous alleles as rice cultivarCalaroma-201. Because the rice variety is essentially homozygous at allrelevant loci, most loci should have only one type of allele present. Incontrast, a genetic marker profile of an F₁ progeny should be the sum ofthose parents, e.g., if one parent was homozygous for allele x at aparticular locus, and the other parent homozygous for allele y at thatlocus, then the F₁ progeny will be xy (heterozygous) at that locus.Subsequent generations of progeny produced by selection and breeding areexpected to be of genotype x (homozygous), y (homozygous), or xy(heterozygous) for that locus position. When the F₁ plant is selfed orsibbed for successive filial generations, the locus should be either xor y for that position.

In addition, plants and plant parts substantially benefiting from theuse of rice cultivar Calaroma-201 in their development, such as ricecultivar Calaroma-201 comprising a gene conversion, backcrossconversion, transgene, or genetic sterility factor, may be identified byhaving a molecular marker profile with a high percent identity to ricecultivar Calaroma-201. Such a percent identity might be 95%, 96%, 97%,98%, 99%, 99.5%, or 99.9% identical to rice cultivar Calaroma-201.

The SSR profile of rice cultivar Calaroma-201 can also be used toidentify essentially derived varieties and other progeny varietiesdeveloped from the use of rice cultivar Calaroma-201, as well as cellsand other plant parts thereof. Such plants may be developed using themarkers identified in WO 00/31964, U.S. Pat. Nos. 6,162,967, and7,288,386. Progeny plants and plant parts produced using rice cultivarCalaroma-201 may be identified by having a molecular marker profile ofat least 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 76%,77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%,91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 99.5% geneticcontribution from rice cultivar Calaroma-201, as measured by eitherpercent identity or percent similarity. Such progeny may be furthercharacterized as being within a pedigree distance of rice cultivarCalaroma-201, such as within 1, 2, 3, 4, or 5 or less cross-pollinationsto a rice plant other than rice cultivar Calaroma-201 or a plant thathas rice cultivar Calaroma-201 as a progenitor. Unique molecularprofiles may be identified with other molecular tools such as SNPs andRFLPs.

While determining the genotypic profile of the plants described supra,several unique SSR profiles may also be identified which did not appearin either parent of such plant. Such unique SSR profiles may ariseduring the breeding process from recombination or mutation. Acombination of several unique alleles provides a means of identifying aplant variety, an F₁ progeny produced from such variety, and progenyproduced from such variety.

Molecular data from Calaroma-201 may be used in a plant breedingprocess. Nucleic acids may be isolated from a seed of Calaroma-201 orfrom a plant, plant part, or cell produced by growing a seed ofCalaroma-201, or from a seed of Calaroma-201 with a gene conversion, orfrom a plant, plant part, or cell of Calaroma-201 with a geneconversion. One or more polymorphisms may be isolated from the nucleicacids. A plant having one or more of the identified polymorphisms may beselected and used in a plant breeding method to produce another plant.

Introduction of a New Trait or Locus into Rice Cultivar Calaroma-201

Cultivar Calaroma-201 represents a new base genetic variety into which anew gene, locus or trait may be introgressed. Backcrossing and directtransformation represent two important methods that can be used toaccomplish such an introgression.

Single or Multiple Gene (Locus) Conversions

When the term “rice plant” is used in the context of the presentinvention, this also includes any single or multiple gene or locusconversions of that variety. The term “single locus converted plant” or“single gene converted plant” refers to those rice plants which aredeveloped by backcrossing or genetic engineering, wherein essentiallyall of the desired morphological and physiological characteristics of avariety are recovered in addition to the one or more genes transferredinto the variety via the backcrossing technique or genetic engineering.Backcrossing methods can be used with the present invention to improveor introduce a characteristic into the variety.

A backcross conversion of rice cultivar Calaroma-201 occurs when DNAsequences are introduced through backcrossing (Hallauer, et al., “CornBreeding,” Corn and Corn Improvements, No. 18, pp. 463-481 (1988)), withrice cultivar Calaroma-201 utilized as the recurrent parent. Bothnaturally occurring and transgenic DNA sequences may be introducedthrough backcrossing techniques. A backcross conversion may produce aplant with a trait or locus conversion in at least two or morebackcrosses, including at least 2 crosses, at least 3 crosses, at least4 crosses, at least 5 crosses, and the like. Molecular marker assistedbreeding or selection may be utilized to reduce the number ofbackcrosses necessary to achieve the backcross conversion. For example,see, Openshaw, S. J., et al., Marker-assisted Selection in BackcrossBreeding, Proceedings Symposium of the Analysis of Molecular Data, CropScience Society of America, Corvallis, Oreg. (August 1994), where it isdemonstrated that a backcross conversion can be made in as few as twobackcrosses.

The complexity of the backcross conversion method depends on the type oftrait being transferred (single genes or closely linked genes ascompared to unlinked genes), the level of expression of the trait, thetype of inheritance (cytoplasmic or nuclear), and the types of parentsincluded in the cross. It is understood by those of ordinary skill inthe art that for single gene traits that are relatively easy toclassify, the backcross method is effective and relatively easy tomanage. (See, Hallauer, et al., Corn and Corn Improvement, Sprague andDudley, Third Ed. (1998)). Desired traits that may be transferredthrough backcross conversion include, but are not limited to, sterility(nuclear and cytoplasmic), fertility restoration, nutritionalenhancements, drought tolerance, nitrogen utilization, altered fattyacid profile, modified fatty acid metabolism, modified carbohydratemetabolism, industrial enhancements, yield stability, yield enhancement,disease resistance (bacterial, fungal, or viral), insect resistance, andherbicide resistance. In addition, an introgression site itself, such asan FRT site, Lox site, or other site specific integration site, may beinserted by backcrossing and utilized for direct insertion of one ormore genes of interest into a specific plant variety.

A single locus may contain several transgenes, such as a transgene fordisease resistance that, in the same expression vector, also contains atransgene for herbicide resistance. The gene for herbicide resistancemay be used as a selectable marker and/or as a phenotypic trait. Asingle locus conversion of site specific integration system allows forthe integration of multiple genes at a known recombination site in thegenome. At least one, at least two or at least three and less than ten,less than nine, less than eight, less than seven, less than six, lessthan five or less than four locus conversions may be introduced into theplant by backcrossing, introgression or transformation to express thedesired trait, while the plant, or a plant grown from the seed, plantpart or plant cell, otherwise retains the phenotypic characteristics ofthe deposited seed when grown under the same environmental conditions.

The backcross conversion may result from either the transfer of adominant allele or a recessive allele. Selection of progeny containingthe trait of interest is accomplished by direct selection for a traitassociated with a dominant allele. Transgenes transferred viabackcrossing typically function as a dominant single gene trait and arerelatively easy to classify. Selection of progeny for a trait that istransferred via a recessive allele requires growing and selfing thefirst backcross generation to determine which plants carry the recessivealleles. Recessive traits may require additional progeny testing insuccessive backcross generations to determine the presence of the locusof interest. The last backcross generation is usually selfed to givepure breeding progeny for the gene(s) being transferred, although abackcross conversion with a stably introgressed trait may also bemaintained by further backcrossing to the recurrent parent withselection for the converted trait.

Along with selection for the trait of interest, progeny are selected forthe phenotype of the recurrent parent. The backcross is a form ofinbreeding, and the features of the recurrent parent are automaticallyrecovered after successive backcrosses. Poehlman, Breeding Field Crops,p. 204 (1987). Poehlman suggests from one to four or more backcrosses,but as noted above, the number of backcrosses necessary can be reducedwith the use of molecular markers. Other factors, such as a geneticallysimilar donor parent, may also reduce the number of backcrossesnecessary. As noted by Poehlman, backcrossing is easiest for simplyinherited, dominant, and easily recognized traits.

One process for adding or modifying a trait or locus in rice cultivarCalaroma-201 comprises crossing rice cultivar Calaroma-201 plants grownfrom rice cultivar Calaroma-201 seed with plants of another rice varietythat comprise the desired trait, gene or locus, selecting F₁ progenyplants that comprise the desired trait, gene or locus to produceselected F₁ progeny plants, crossing the selected progeny plants withthe rice cultivar Calaroma-201 plants to produce backcross progenyplants, selecting for backcross progeny plants that have the desiredtrait, gene or locus and the morphological characteristics of ricecultivar Calaroma-201 to produce selected backcross progeny plants, andbackcrossing to rice cultivar Calaroma-201 two or more times insuccession to produce selected third or higher backcross progeny plantsthat comprise said trait, gene or locus. The modified rice cultivarCalaroma-201 may be further characterized as having the physiologicaland morphological characteristics of rice cultivar Calaroma-201 listedin Table 1 as determined at the 5% significance level when grown in thesame environmental conditions and/or may be characterized by percentsimilarity or identity to rice cultivar Calaroma-201 as determined bySSR markers. The above method may be utilized with fewer backcrosses inappropriate situations, such as when the donor parent is highly relatedor markers are used in the selection step. Desired traits that may beused include those nucleic acids known in the art, some of which arelisted herein, that will affect traits through nucleic acid expressionor inhibition. Desired loci include the introgression of FRT, Lox, andother sites for site specific integration, which may also affect adesired trait if a functional nucleic acid is inserted at theintegration site.

In addition, the above process and other similar processes describedherein may be used to produce first generation progeny rice seed byadding a step at the end of the process that comprises crossing ricecultivar Calaroma-201 with the introgressed trait or locus with adifferent rice plant and harvesting the resultant first generationprogeny rice seed.

Methods for Genetic Engineering of Rice

With the advent of molecular biological techniques that have allowed theisolation and characterization of genes that encode specific proteinproducts, scientists in the field of plant biology developed a stronginterest in engineering the genome of plants (genetic engineering) tocontain and express foreign genes, or additional, or modified versionsof native, or endogenous genes (perhaps driven by different promoters)in order to alter the traits of a plant in a specific manner. Plantsaltered by genetic engineering are often referred to as ‘geneticallymodified’. Any DNA sequences, whether from a different species or fromthe same species, which are introduced into the genome usingtransformation and/or various breeding methods, are referred to hereincollectively as “transgenes.” Over the last fifteen to twenty yearsseveral methods for producing transgenic plants have been developed, andthe present invention, in particular embodiments, also relates totransformed versions of the claimed cultivar.

Vectors used for the transformation of rice cells are not limited solong as the vector can express an inserted DNA in the cells. Forexample, vectors comprising promoters for constitutive gene expressionin rice cells (e.g., cauliflower mosaic virus 35S promoter) andpromoters inducible by exogenous stimuli can be used. Examples ofsuitable vectors include pBI binary vector. The “rice cell” into whichthe vector is to be introduced includes various forms of rice cells,such as cultured cell suspensions, protoplasts, leaf sections, andcallus. A vector can be introduced into rice cells by known methods,such as the polyethylene glycol method, polycation method,electroporation, Agrobacterium-mediated transfer, particle bombardmentand direct DNA uptake by protoplasts. See, e.g., Pang et al. (The PlantJ., 9, 899-909, 1996).

Numerous methods for plant transformation have been developed, includingbiological and physical, plant transformation protocols. See, forexample, Miki, et al., “Procedures for Introducing Foreign DNA intoPlants” in Methods in Plant Molecular Biology and Biotechnology, Glickand Thompson (Eds.), CRC Press, Inc., Boca Raton, pp. 67-88 (1993). Inaddition, expression vectors and in vitro culture methods for plant cellor tissue transformation and regeneration of plants are available. See,for example, Gruber, et al., “Vectors for Plant Transformation” inMethods in Plant Molecular Biology and Biotechnology, Glick and Thompson(Eds.), CRC Press, Inc., Boca Raton, pp. 89-119 (1993).

A. Agrobacterium-Mediated Transformation:

One method for introducing an expression vector into plants is based onthe natural transformation system of Agrobacterium. See, for example,Horsch, et al., Science, 227:1229 (1985). A. tumefaciens and A.rhizogenes are plant pathogenic soil bacteria which geneticallytransform plant cells. The Ti and Ri plasmids of A. tumefaciens and A.rhizogenes, respectively, carry genes responsible for genetictransformation of the plant. See, for example, Kado, C. I., Crit. Rev.Plant Sci., 10:1 (1991). Descriptions of Agrobacterium vector systemsand methods for Agrobacterium-mediated gene transfer are provided byGruber, et al., supra, Miki, et al., supra, and Moloney, et al., PlantCell Rep., 8:238 (1989). See also, U.S. Pat. No. 5,563,055 (Townsend andThomas), issued Oct. 8, 1996.

Agrobacterium-mediated transfer is a widely applicable system forintroducing gene loci into plant cells, including rice. An advantage ofthe technique is that DNA can be introduced into whole plant tissues,thereby bypassing the need for regeneration of an intact plant from aprotoplast. Modern Agrobacterium transformation vectors are capable ofreplication in E. coli as well as Agrobacterium, allowing for convenientmanipulations (Klee et al., Bio. Tech., 3(7):637-642, 1985). Moreover,recent technological advances in vectors for Agrobacterium-mediated genetransfer have improved the arrangement of genes and restriction sites inthe vectors to facilitate the construction of vectors capable ofexpressing various polypeptide coding genes. The vectors described haveconvenient multi-linker regions flanked by a promoter and apolyadenylation site for direct expression of inserted polypeptidecoding genes. Additionally, Agrobacterium containing both armed anddisarmed Ti genes can be used for transformation.

In those plant strains where Agrobacterium-mediated transformation isefficient, it is the method of choice because of the facile and definednature of the gene locus transfer. The use of Agrobacterium-mediatedplant integrating vectors to introduce DNA into plant cells is wellknown in the art (Fraley et al., Bio. Tech., 3(7):629-635, 1985; U.S.Pat. No. 5,563,055). For example, U.S. Pat. No. 5,349,124 describes amethod of transforming rice plant cells using Agrobacterium-mediatedtransformation. By inserting a chimeric gene having a DNA codingsequence encoding for the full-length B.t. toxin protein that expressesa protein toxic toward Lepidopteran larvae, this methodology resulted inrice having resistance to such insects.

B. Direct Gene Transfer:

Several methods of plant transformation, collectively referred to asdirect gene transfer, have been developed as an alternative toAgrobacterium-mediated transformation. A generally applicable method fordelivering transforming DNA segments to plant cells ismicroprojectile-mediated transformation, or microprojectile bombardment.In this method, particles are coated with nucleic acids and deliveredinto cells by a propelling force. Sanford, et al., Part. Sci. Technol.,5:27 (1987); Sanford, J. C., Trends Biotech., 6:299 (1988); Klein, etal., Bio/technology, 6:559-563 (1988); Sanford, J. C., Physiol Plant,7:206 (1990); Klein, et al., Bio/technology, 10:268 (1992). See also,U.S. Pat. No. 5,015,580 (Christou, et al.), issued May 14, 1991; U.S.Pat. No. 5,322,783 (Tomes, et al.), issued Jun. 21, 1994.

Another method for physical delivery of DNA to plants is sonication oftarget cells. Zhang, et al., Bio/technology, 9:996 (1991).Alternatively, liposome and spheroplast fusion have been used tointroduce expression vectors into plants. Deshayes, et al., EMBO J.,4:2731 (1985); Christou, et al., PNAS, 84:3962 (1987). Direct uptake ofDNA into protoplasts using CaCl₂) precipitation, calcium phosphateprecipitation, polyethylene glycol treatment, polyvinyl alcohol, orpoly-L-ornithine has also been reported. See, e.g., Potrykus et al.,Mol. Gen. Genet., 199:183-188, 1985; Omirulleh et al., Plant Mol. Biol21(3):415-428, 1993; Fromm et al., Nature, 312:791-793, 1986; Uchimiyaet al., Mol. Gen. Genet., 204:204, 1986; Marcotte et al., Nature,335:454, 1988; Hain, et al., Mol. Gen. Genet., 199:161, 1985 and Draper,et al., Plant Cell Physiol. 23:451, 1982.

Electroporation of protoplasts and whole cells and tissues has also beendescribed. Donn, et al., In Abstracts of VIIth International Congress onPlant Cell and Tissue Culture IAPTC, A2-38, p. 53, 1990; D'Halluin, etal., Plant Cell, 4:1495-1505, 1992; and Spencer, et al., Plant Mol.Biol., 24:51-61, 1994. Another illustrative embodiment of a method fordelivering DNA into plant cells by acceleration is the BiolisticsParticle Delivery System, which can be used to propel particles coatedwith DNA or cells through a screen, such as a stainless steel or Nytexscreen, onto a surface covered with target rice cells.

Transformation of plants and expression of foreign genetic elements isexemplified in Choi et al., Plant Cell Rep., 13: 344-348, 1994 and Ellulet al., Theor. Appl. Genet., 107:462-469, 2003.

Following transformation of rice target tissues, expression ofselectable marker genes allows for preferential selection of transformedcells, tissues, and/or plants, using regeneration and selection methodsnow well known in the art.

The methods described herein for transformation would typically be usedfor producing a transgenic variety. The transgenic variety could then becrossed, with another (non-transformed or transformed) variety, in orderto produce a new transgenic variety. Alternatively, a genetic traitwhich has been engineered into a particular rice cultivar using thetransformation techniques described could be moved into another cultivarusing traditional backcrossing techniques that are well known in theplant breeding arts. For example, a backcrossing approach could be usedto move an engineered trait from a public, non-elite variety into anelite variety, or from a variety containing a foreign gene in its genomeinto a variety or varieties which do not contain that gene. As usedherein, “crossing” can refer to a simple X by Y cross, or the process ofbackcrossing, depending on the context.

Expression Vectors for Rice Transformation: Marker Genes

Expression vectors include at least one genetic marker, operably linkedto a regulatory element (a promoter, for example) that allowstransformed cells containing the marker to be either recovered bynegative selection, i.e., inhibiting growth of cells that do not containthe selectable marker gene, or by positive selection, i.e., screeningfor the product encoded by the genetic marker. Many commonly usedselectable marker genes for plant transformation are well known in thetransformation arts, and include, for example, genes that code forenzymes that metabolically detoxify a selective chemical agent which maybe an antibiotic or a herbicide, or genes that encode an altered targetwhich is insensitive to the inhibitor. A few positive selection methodsare also known in the art.

One commonly used selectable marker gene for plant transformation is theneomycin phosphotransferase II (nptII) gene, isolated from transposonTn5, which when placed under the control of plant regulatory signalswhich confers resistance to kanamycin. Fraley et al., Proc. Natl. Acad.Sci. U.S.A., 80:4803 (1983). Another commonly used selectable markergene is the hygromycin phosphotransferase gene which confers resistanceto the antibiotic hygromycin. Vanden Elzen et al., Plant Mol. Biol.,5:299 (1985).

Additional selectable marker genes of bacterial origin that conferresistance to antibiotics include gentamycin acetyl transferase,streptomycin phosphotransferase, aminoglycoside-3′-adenyl transferase,the bleomycin resistance determinant. Hayford et al., Plant Physiol.86:1216 (1988), Jones et al., Mol. Gen. Genet., 210:86 (1987), Svab etal., Plant Mol. Biol. 14:197 (1990) Hille et al., Plant Mol. Biol. 7:171(1986). Other selectable marker genes confer resistance to herbicidessuch as glyphosate, glufosinate or bromoxynil. Comai et al., Nature317:741-744 (1985), Gordon-Kamm et al., Plant Cell 2:603-618 (1990) andStalker et al., Science 242:419-423 (1988). Selectable marker genes forplant transformation not of bacterial origin include, for example, mousedihydrofolate reductase, plant 5-enolpyruvylshikimate-3-phosphatesynthase and plant acetolactate synthase. Eichholtz et al., Somatic CellMol. Genet. 13:67 (1987), Shah et al., Science 233:478 (1986), Charestet al., Plant Cell Rep. 8:643 (1990).

Another class of marker genes for plant transformation requiresscreening of presumptively transformed plant cells rather than directgenetic selection of transformed cells for resistance to a toxicsubstance such as an antibiotic. These genes are particularly useful toquantify or visualize the spatial pattern of expression of a gene inspecific tissues and are frequently referred to as reporter genesbecause they can be fused to a gene or gene regulatory sequence for theinvestigation of gene expression. Commonly used genes for screeningpresumptively transformed cells include α-glucuronidase (GUS,α-galactosidase, luciferase and chloramphenicol, acetyltransferase.Jefferson, R. A., Plant Mol. Biol. Rep. 5:387 (1987), Teeri et al., EMBOJ. 8:343 (1989), Koncz et al., Proc. Natl. Acad. Sci U.S.A. 84:131(1987), DeBlock et al., EMBO J. 3:1681 (1984).

In vivo methods for visualizing GUS activity that do not requiredestruction of plant tissue are available. Molecular Probes publication2908, IMAGENE GREEN, p. 1-4 (1993) and Naleway et al., J. Cell Biol.115:151a (1991). However, these in vivo methods for visualizing GUSactivity have not proven useful for recovery of transformed cellsbecause of low sensitivity, high fluorescent backgrounds and limitationsassociated with the use of luciferase genes as selectable markers.

More recently, a gene encoding Green Fluorescent Protein (GFP) has beenutilized as a marker for gene expression in prokaryotic and eukaryoticcells. Chalfie et al., Science 263:802 (1994). GFP and mutants of GFPmay be used as screenable markers.

Expression Vectors for Rice Transformation: Promoters

Genes included in expression vectors must be driven by a nucleotidesequence comprising a regulatory element, for example, a promoter.Several types of promoters are now well known in the transformationarts, as are other regulatory elements that can be used alone or incombination with promoters.

As used herein, “promoter” includes reference to a region of DNAupstream from the start of transcription and involved in recognition andbinding of RNA polymerase and other proteins to initiate transcription.A “plant promoter” is a promoter capable of initiating transcription inplant cells. Examples of promoters under developmental control includepromoters that preferentially initiate transcription in certain tissues,such as leaves, roots, seeds, fibers, xylem vessels, tracheids, orsclerenchyma. Such promoters are referred to as “tissue-preferred”.Promoters which initiate transcription only in certain tissue arereferred to as “tissue-specific”. A “cell type” specific promoterprimarily drives expression in certain cell types in one or more organs,for example, vascular cells in roots or leaves. An “inducible” promoteris a promoter which is under environmental control. Examples ofenvironmental conditions that may effect transcription by induciblepromoters include anaerobic conditions or the presence of light.Tissue-specific, tissue-preferred, cell type specific, and induciblepromoters constitute the class of “non-constitutive” promoters. A“constitutive” promoter is a promoter which is active under mostenvironmental conditions.

A. Inducible Promoters:

An inducible promoter is operably linked to a gene for expression inrice. Optionally, the inducible promoter is operably linked to anucleotide sequence encoding a signal sequence which is operably linkedto a gene for expression in rice. With an inducible promoter the rate oftranscription increases in response to an inducing agent.

Any inducible promoter can be used in the instant invention. See Ward etal., Plant Mol. Biol. 22:361-366 (1993). Exemplary inducible promotersinclude, but are not limited to, that from the ACEI system whichresponds to copper (Meft et al., PNAS 90:4567-4571 (1993)); In2 genefrom maize which responds to benzenesulfonamide herbicide safeners(Hershey et al., Mol. Gen Genetics 227:229-237 (1991) and Gatz et al.,Mol. Gen. Genetics 243:32-38 (1994)) or Tet repressor from Tn10 (Gatz etal., Mol. Gen. Genetics 227:229-237 (1991). A particularly preferredinducible promoter is a promoter that responds to an inducing agent towhich plants do not normally respond. An exemplary inducible promoter isthe inducible promoter from a steroid hormone gene, the transcriptionalactivity of which is induced by a glucocorticosteroid hormone. Schena etal., Proc. Natl. Acad. Sci. U.S.A. 88:0421 (1991).

B. Constitutive Promoters:

A constitutive promoter is operably linked to a gene for expression inrice or the constitutive promoter is operably linked to a nucleotidesequence encoding a signal sequence which is operably linked to a genefor expression in rice.

Many different constitutive promoters can be utilized in the instantinvention. Exemplary constitutive promoters include, but are not limitedto, the promoters from plant viruses such as the 35S promoter from CaMV(Odell et al., Nature 313:810-812 (1985) and the promoters from suchgenes as rice actin (McElroy et al., Plant Cell 2:163-171 (1990));ubiquitin (Christensen et al., Plant Mol. Biol. 12:619-632 (1989) andChristensen et al., Plant Mol. Biol. 18:675-689 (1992)); pEMU (Last etal., Theor. Appl. Genet. 81:581-588 (1991)); MAS (Velten et al., EMBO J.3:2723-2730 (1984)) and maize H3 histone (Lepetit et al., Mol. Gen.Genetics 231:276-285 (1992) and Atanassova et al., Plant Journal 2 (3):291-300 (1992)). The ALS promoter, Xba1/Nco1 fragment 5′ to the Brassicanapus ALS3 structural gene (or a nucleotide sequence similarity to saidXba1/Nco1 fragment), represents a particularly useful constitutivepromoter. See PCT application WO 96/30530.

C. Tissue-Specific or Tissue-Preferred Promoters:

A tissue-specific promoter is operably linked to a gene for expressionin rice. Optionally, the tissue-specific promoter is operably linked toa nucleotide sequence encoding a signal sequence which is operablylinked to a gene for expression in rice. Plants transformed with a geneof interest operably linked to a tissue-specific promoter produce theprotein product of the transgene exclusively, or preferentially, in aspecific tissue.

Any tissue-specific or tissue-preferred promoter can be utilized in theinstant invention. Exemplary tissue-specific or tissue-preferredpromoters include, but are not limited to, a root-preferred promoter,such as that from the phaseolin gene (Murai et al., Science 23:476-482(1983) and Sengupta-Gopalan et al., Proc. Natl. Acad. Sci. U.S.A.82:3320-3324 (1985)); a leaf-specific and light-induced promoter such asthat from cab or rubisco (Simpson et al., EMBO J. 4(11):2723-2729 (1985)and Timko et al., Nature 318:579-582 (1985)); an anther-specificpromoter such as that from LAT52 (Twell et al., Mol. Gen. Genetics217:240-245 (1989)); a pollen-specific promoter such as that from Zm13(Guerrero et al., Mol. Gen. Genetics 244:161-168 (1993)) or amicrospore-preferred promoter such as that from apg (Twell et al., Sex.Plant Reprod. 6:217-224 (1993)).

Signal Sequences for Targeting Proteins to Subcellular Compartments

Transport of protein produced by transgenes to a subcellular compartmentsuch as the chloroplast, vacuole, peroxisome, glyoxysome, cell wall ormitochondrion or for secretion into the apoplast, is accomplished bymeans of operably linking the nucleotide sequence encoding a signalsequence to the 5′ and/or 3′ region of a gene encoding the protein ofinterest. Targeting sequences at the 5′ and/or 3′ end of the structuralgene may determine, during protein synthesis and processing, where theencoded protein is ultimately compartmentalized.

The presence of a signal sequence directs a polypeptide to either anintracellular organelle or subcellular compartment or for secretion tothe apoplast. Many signal sequences are known in the art. See, forexample Becker et al., Plant Mol. Biol. 20:49 (1992), Close, P. S.,Master's Thesis, Iowa State University (1993), Knox, C., et al.,“Structure and Organization of Two Divergent Alpha-Amylase Genes fromBarley”, Plant Mol. Biol. 9:3-17 (1987), Lerner et al., Plant Physiol.91:124-129 (1989), Fontes et al., Plant Cell 3:483-496 (1991), Matsuokaet al., Proc. Natl. Acad. Sci. 88:834 (1991), Gould et al., J. Cell.Biol. 108:1657 (1989), Creissen et al., Plant J. 2:129 (1991), Kalderon,et al., A short amino acid sequence able to specify nuclear location,Cell 39:499-509 (1984), Steifel, et al., Expression of a maize cell wallhydroxyproline-rich glycoprotein gene in early leaf and root vasculardifferentiation, Plant Cell 2:785-793 (1990).

Additional Methods for Genetic Engineering of Rice

In general, methods to transform, modify, edit or alter plant endogenousgenomic DNA include altering the plant native DNA sequence or apre-existing transgenic sequence including regulatory elements, codingand non-coding sequences. These methods can be used, for example, totarget nucleic acids to pre-engineered target recognition sequences inthe genome. Such pre-engineered target sequences may be introduced bygenome editing or modification. As an example, a genetically modifiedplant variety can be generated using “custom” or engineeredendonucleases such as meganucleases produced to modify plant genomes(see e.g., WO 2009/114321; Gao et al. (2010) Plant Journal 1:176-187).Another site-directed engineering method is through the use of zincfinger domain recognition coupled with the restriction properties ofrestriction enzyme. See e.g., Urnov, et al., (2010) Nat Rev Genet.11(9):636-46; Shukla, et al., (2009) Nature 459 (7245):437-41. Atranscription activator-like (TAL) effector-DNA modifying enzyme (TALEor TALEN) is also used to engineer changes in plant genome. See e.g.,US20110145940, Cermak et al., (2011) Nucleic Acids Res. 39(12) and Bochet al., (2009), Science 326(5959): 1509-12. Site-specific modificationof plant genomes can also be performed using the bacterial type IICRISPR (clustered regularly interspaced short palindromic repeats)/Cas(CRISPR-associated) system, as well as similar CRISPR relatedtechnologies including but not limited to use of enzymes Cpf1 and Cms1.See e.g., Belhaj et al., (2013), Plant Methods 9: 39; The Cas9/guideRNA-based system allows targeted cleavage of genomic DNA guided by acustomizable small noncoding RNA in plants (see e.g., WO 2015026883A1,incorporated herein by reference).

Many techniques for gene silencing are well known to one of skill in theart, including, but not limited to, knock-outs (such as by insertion ofa transposable element such as mu (Vicki Chandler, The Maize Handbook,Ch. 118 (Springer-Verlag 1994)) or other genetic elements such as a FRTand Lox that are used for site specific integrations, antisensetechnology (see, e.g., Sheehy, et al., PNAS USA, 85:8805-8809 (1988);and U.S. Pat. Nos. 5,107,065, 5,453,566, and 5,759,829); co-suppression(e.g., Taylor, Plant Cell, 9:1245 (1997); Jorgensen, Trends Biotech.,8(12):340-344 (1990); Flavell, PNAS USA, 91:3490-3496 (1994); Finnegan,et al., Bio/Technology, 12:883-888 (1994); Neuhuber, et al., Mol. Gen.Genet., 244:230-241 (1994)); RNA interference (Napoli, et al., PlantCell, 2:279-289 (1990); U.S. Pat. No. 5,034,323; Sharp, Genes Dev.,13:139-141 (1999); Zamore, et al., Cell, 101:25-33 (2000); Montgomery,et al., PNAS USA, 95:15502-15507 (1998)), virus-induced gene silencing(Burton, et al., Plant Cell, 12:691-705 (2000); Baulcombe, Curr. Op.Plant Bio., 2:109-113 (1999)); target-RNA-specific ribozymes (Haseloff,et al., Nature, 334: 585-591 (1988)); hairpin structures (Smith, et al.,Nature, 407:319-320 (2000); WO 99/53050; WO 98/53083); MicroRNA(Aukerman & Sakai, Plant Cell, 15:2730-2741 (2003)); ribozymes(Steinecke, et al., EMBO J., 11:1525 (1992); Perriman, et al., AntisenseRes. Dev., 3:253 (1993)); oligonucleotide mediated targeted modification(e.g., WO 03/076574 and WO 99/25853); Zn-finger targeted molecules(e.g., WO 01/52620, WO 03/048345, and WO 00/42219); and other methods orcombinations of the above methods known to those of skill in the art.

A genetic map can be generated that identifies the approximatechromosomal location of an integrated DNA molecule, for example viaconventional restriction fragment length polymorphisms (RFLP),polymerase chain reaction (PCR) analysis, simple sequence repeats (SSR),and single nucleotide polymorphisms (SNP). For exemplary methodologiesin this regard, see Glick and Thompson, Methods in Plant MolecularBiology and Biotechnology, pp. 269-284 (CRC Press, Boca Raton, 1993).

Wang et al. discuss “Large Scale Identification, Mapping and Genotypingof Single-Nucleotide Polymorphisms in the Human Genome”, Science (1998)280:1077-1082, and similar capabilities are increasingly available forthe rice genome. Map information concerning chromosomal location isuseful for proprietary protection of a subject transgenic plant. Ifunauthorized propagation is undertaken and crosses made with othergermplasm, the map of the integration region can be compared to similarmaps for suspect plants to determine if the latter have a commonparentage with the subject plant. Map comparisons could involvehybridizations, RFLP, PCR, SSR, sequencing or combinations thereof, allof which are conventional techniques. SNPs may also be used alone or incombination with other techniques.

Rice Cultivar Calaroma-201 Further Comprising a Transgene

Transgenes and transformation methods provide means to engineer thegenome of plants to contain and express heterologous genetic elements,including but not limited to foreign genetic elements, additional copiesof endogenous elements, and/or modified versions of native or endogenousgenetic elements, in order to alter at least one trait of a plant in aspecific manner. Any heterologous DNA sequence(s), whether from adifferent species or from the same species, which are inserted into thegenome using transformation, backcrossing, or other methods known to oneof skill in the art are referred to herein collectively as transgenes.The sequences are heterologous based on sequence source, location ofintegration, operably linked elements, or any combination thereof. Oneor more transgenes of interest can be introduced into rice cultivarCalaroma-201. Transgenic variants of rice cultivar Calaroma-201 plants,seeds, cells, and parts thereof or derived therefrom are provided.Transgenic variants of Calaroma-201 comprise the physiological andmorphological characteristics of rice cultivar Calaroma-201, such aslisted in Table 1 as determined at the 5% significance level when grownin the same environmental conditions, and/or may be characterized oridentified by percent similarity or identity to Calaroma-201 asdetermined by SSR or other molecular markers. In some examples,transgenic variants of rice cultivar Calaroma-201 are produced byintroducing at least one transgene of interest into rice cultivarCalaroma-201 by transforming Calaroma-201 with a polynucleotidecomprising the transgene of interest. In other examples, transgenicvariants of rice cultivar Calaroma-201 are produced by introducing atleast one transgene by introgressing the transgene into rice cultivarCalaroma-201 by crossing.

In one example, a process for modifying rice cultivar Calaroma-201 withthe addition of a desired trait, said process comprising transforming arice plant of cultivar Calaroma-201 with a transgene that confers adesired trait is provided. Therefore, transgenic Calaroma-201 ricecells, plants, plant parts, and seeds produced from this process areprovided. In some examples one more desired traits may include traitssuch as sterility (nuclear and cytoplasmic), fertility restoration,nutritional enhancements, drought tolerance, nitrogen utilization,altered fatty acid profile, modified fatty acid metabolism, modifiedcarbohydrate metabolism, industrial enhancements, yield stability, yieldenhancement, disease resistance (bacterial, fungal, or viral), insectresistance, and herbicide resistance. The specific gene may be any knownin the art or listed herein, including but not limited to apolynucleotide conferring resistance to an ALS-inhibitor herbicide,imidazolinone, sulfonylurea, protoporphyrinogen oxidase (PPO)inhibitors, hydroxyphenyl pyruvate dioxygenase (HPPD) inhibitors,glyphosate, glufosinate, triazine, 2,4-dichlorophenoxyacetic acid(2,4-D), dicamba, broxynil, metribuzin, or benzonitrile herbicides; apolynucleotide encoding a Bacillus thuringiensis polypeptide, apolynucleotide encoding a phytase, a fatty acid desaturase (e.g., FAD-2,FAD-3), galactinol synthase, a raffinose synthetic enzyme; or apolynucleotide conferring resistance to tipburn, Fusarium oxysporum,Nasonovia ribisnigri, Sclerotinia sclerotiorum or other plant pathogens.

Foreign Protein Genes and Agronomic Genes

By means of the present invention, plants can be genetically engineeredto express various phenotypes of agronomic interest. Through thetransformation of rice, the expression of genes can be altered toenhance disease resistance, insect resistance, herbicide resistance,agronomic, nutritional quality, and other traits. Transformation canalso be used to insert DNA sequences which control or help controlmale-sterility. DNA sequences native to rice, as well as non-native DNAsequences, can be transformed into rice and used to alter levels ofnative or non-native proteins. Various promoters, targeting sequences,enhancing sequences, and other DNA sequences can be inserted into thegenome for the purpose of altering the expression of proteins. Reductionof the activity of specific genes (also known as gene silencing or genesuppression) is desirable for several aspects of genetic engineering inplants.

Likewise, by means of the present invention, agronomic genes can beexpressed in transformed plants. More particularly, plants can begenetically engineered to express various phenotypes of agronomicinterest. Exemplary nucleotide sequences and/or native loci that conferat least one trait of interest, which optionally may be conferred oraltered by genetic engineering, transformation or introgression of atransformed event include, but are not limited to, those categorizedbelow:

1. Genes that Confer Resistance to Pests or Disease and that Encode:

A. Plant disease resistance genes. Plant defenses are often activated byspecific interaction between the product of a disease resistance gene(R) in the plant and the product of a corresponding avirulence (Avr)gene in the pathogen. A plant line can be transformed with a clonedresistance gene to engineer plants that are resistant to specificpathogen strains. See, for example Jones et al., Science 266:789 (1994)(cloning of the tomato Cf-9 gene for resistance to Cladosporium fulvum);Martin et al., Science 262:1432 (1993) (tomato Pto gene for resistanceto Pseudomonas syringae pv. Tomato encodes a protein kinase); Mindrinoset al., Cell 78:1089 (1994) (Arabidopsis RSP2 gene for resistance toPseudomonas syringae).

B. A Bacillus thuringiensis protein, a derivative thereof or a syntheticpolypeptide modeled thereon. See, for example, Geiser et al., Gene48:109 (1986), who disclose the cloning and nucleotide sequence of a Btδ-endotoxin gene. Moreover, DNA molecules encoding 6-endotoxin genes canbe purchased from American Type Culture Collection, Manassas, Va., forexample, under ATCC Accession Nos. 40098, 67136, 31995 and 31998.

C. A lectin. See, for example, the disclosure by Van Damme et al., PlantMolec. Biol. 24:25 (1994), who disclose the nucleotide sequences ofseveral Clivia miniata mannose-binding lectin genes.

D. A vitamin-binding protein such as avidin. See PCT applicationUS93/06487, the contents of which are hereby incorporated by reference.The application teaches the use of avidin and avidin homologues aslarvicides against insect pests.

E. An enzyme inhibitor, for example, a protease or proteinase inhibitoror an amylase inhibitor. See, for example, Abe et al., J. Biol. Chem.262:16793 (1987) (nucleotide sequence of rice cysteine proteinaseinhibitor), Huub et al., Plant Molec. Biol. 21:985 (1993) (nucleotidesequence of cDNA encoding tobacco proteinase inhibitor I), Sumitani etal., Biosci. Biotech. Biochem. 57:1243 (1993) (nucleotide sequence ofStreptomyces nitrosporeus α-amylase inhibitor).

F. An insect-specific hormone or pheromone such as an ecdysteroid andjuvenile hormone, a variant thereof, a mimetic based thereon, or anantagonist or agonist thereof. See, for example, the disclosure byHammock et al., Nature 344:458 (1990), of baculovirus expression ofcloned juvenile hormone esterase, an inactivator of juvenile hormone.

G. An insect-specific peptide or neuropeptide which, upon expression,disrupts the physiology of the affected pest. For example, see thedisclosures of Regan, J. Biol. Chem. 269:9 (1994) (expression cloningyields DNA coding for insect diuretic hormone receptor), and Pratt etal., Biochem. Biophys. Res. Comm. 163:1243 (1989) (an allostatin isidentified in Diploptera puntata). See also U.S. Pat. No. 5,266,317 toTomalski et al., who disclose genes encoding insect-specific, paralyticneurotoxins.

H. An insect-specific venom produced in nature by a snake, a wasp, etc.For example, see Pang et al., Gene 116:165 (1992), for disclosure ofheterologous expression in plants of a gene coding for a scorpioninsectotoxic peptide.

I. An enzyme responsible for a hyper accumulation of a monoterpene, asesquiterpene, a steroid, hydroxamic acid, a phenylpropanoid derivativeor another non-protein molecule with insecticidal activity.

J. An enzyme involved in the modification, including thepost-translational modification, of a biologically active molecule; forexample, a glycolytic enzyme, a proteolytic enzyme, a lipolytic enzyme,a nuclease, a cyclase, a transaminase, an esterase, a hydrolase, aphosphatase, a kinase, a phosphorylase, a polymerase, an elastase, achitinase and a glucanase, whether natural or synthetic. See PCTapplication WO 93/02197 in the name of Scott et al., which discloses thenucleotide sequence of a callase gene. DNA molecules which containchitinase-encoding sequences can be obtained, for example, from ATCCunder Accession Nos. 39637 and 67152. See also Kramer et al., InsectBiochem. Molec. Biol. 23:691 (1993), who teach the nucleotide sequenceof a cDNA encoding tobacco hookworm chitinase, and Kawalleck et al.,Plant Molec. Biol. 21:673 (1993), who provide the nucleotide sequence ofthe parsley ubi4-2 polyubiquitin gene.

K. A molecule that stimulates signal transduction. For example, see thedisclosure by Botella et al., Plant Molec. Biol. 24:757 (1994), ofnucleotide sequences for mung bean calmodulin cDNA clones, and Griess etal., Plant Physiol. 104:1467 (1994), who provide the nucleotide sequenceof a maize calmodulin cDNA clone.

L. A hydrophobic moment peptide. See PCT application WO 95/16776(disclosure of peptide derivatives of Tachyplesin which inhibit fungalplant pathogens) and PCT application WO 95/18855 (teaches syntheticantimicrobial peptides that confer disease resistance), the respectivecontents of which are hereby incorporated by reference.

M. A membrane permease, a channel former or a channel blocker. Forexample, see the disclosure of Jaynes et al., Plant Sci 89:43 (1993), ofheterologous expression of a cecropin-β, lytic peptide analog to rendertransgenic tobacco plants resistant to Pseudomonas solanacearum.

N. A viral-invasive protein or a complex toxin derived therefrom. Forexample, the accumulation of viral coat proteins in transformed plantcells imparts resistance to viral infection and/or disease developmenteffected by the virus from which the coat protein gene is derived, aswell as by related viruses. See Beachy et al., Ann. rev. Phytopathol.28:451 (1990). Coat protein-mediated resistance has been conferred upontransformed plants against alfalfa mosaic virus, cucumber mosaic virus,tobacco streak virus, potato virus X, potato virus Y, tobacco etchvirus, tobacco rattle virus and tobacco mosaic virus. Id.

0. An insect-specific antibody or an immunotoxin derived therefrom.Thus, an antibody targeted to a critical metabolic function in theinsect gut would inactivate an affected enzyme, killing the insect. Cf.Taylor et al., Abstract #497, Seventh Int'l Symposium on MolecularPlant-Microbe Interactions (Edinburgh, Scotland) (1994) (enzymaticinactivation in transgenic tobacco via production of single-chainantibody fragments).

P. A virus-specific antibody. See, for example, Tavladoraki et al.,Nature 366:469 (1993), who show that transgenic plants expressingrecombinant antibody genes are protected from virus attack.

Q. A developmental-arrestive protein produced in nature by a pathogen ora parasite. Thus, fungal endo α-1, 4-D-polygalacturonases facilitatefungal colonization and plant nutrient release by solubilizing plantcell wall homo-α-1,4-D-galacturonase. See Lamb et al., Bio/Technology10:1436 (1992). The cloning and characterization of a gene which encodesa celery endopolygalacturonase-inhibiting protein is described byToubart et al., Plant J. 2:367 (1992).

R. A developmental-arrestive protein produced in nature by a plant. Forexample, Logemann et al., Bio/Technology 10:305 (1992), have shown thattransgenic plants expressing the barley ribosome-inactivating gene havean increased resistance to fungal disease.

S. A lettuce mosaic potyvirus (LMV) coat protein gene introduced intorice in order to increase its resistance to LMV infection. See Dinant etal., Molecular Breeding. 1997, 3: 1, 75-86.

T. Genes involved in the Systemic Acquired Resistance (SAR) Responseand/or the pathogenesis-related genes. Briggs, S., Current Biology, 5(2)(1995).

U. Antifungal genes. See Cornelissen and Melchers, Plant Physiol.,101:709-712 (1993); Parijs et al., Planta 183:258-264 (1991) andBushnell et al., Can. J. of Plant Path. 20(2):137-149 (1998).

V. Genes that confer resistance to Phytophthora root rot, such as theRps 1, Rps 1-a, Rps 1-b, Rps 1-c, Rps 1-d, Rps 1-e, Rps 1-k, Rps 2, Rps3-a, Rps 3-b, Rps 3-c, Rps 4, Rps 5, Rps 6, Rps 7 and other Rps genes.See, for example, Shoemaker et al., Phytophthora Root Rot ResistanceGene Mapping in Soybean, Plant Genome IV Conference, San Diego, Calif.(1995).

2. Genes that Confer Resistance to an Herbicide:

A. An herbicide that inhibits the growing point or meristem, such as animidazolinone or a sulfonylurea. Exemplary genes in this category codefor mutant ALS and AHAS enzyme as described, for example, by Lee et al.,EMBO J. 7:1241 (1988), and Miki et al., Theor. Appl. Genet. 80:449(1990), respectively.

B. Glyphosate (resistance impaired by mutant5-enolpyruvlshikimate-3-phosphate synthase (EPSPS) and aroA genes,respectively) and other phosphono compounds such as glufosinate(phosphinothricin acetyl transferase, PAT and Streptomyces hygroscopicusphosphinothricin-acetyl transferase, bar, genes), and pyridinoxy orphenoxy proprionic acids and cyclohexones (ACCase inhibitor-encodinggenes). See, for example, U.S. Pat. No. 4,940,835 to Shah, et al., whichdiscloses the nucleotide sequence of a form of EPSPs which can conferglyphosate resistance. A DNA molecule encoding a mutant aroA gene can beobtained under ATCC accession number 39256, and the nucleotide sequenceof the mutant gene is disclosed in U.S. Pat. No. 4,769,061 to Comai. Seealso Umaballava-Mobapathie in Transgenic Research. 1999, 8: 1, 33-44that discloses Lactuca sativa resistant to glufosinate. European patentapplication No. 0 333 033 to Kumada et al., and U.S. Pat. No. 4,975,374to Goodman et al., disclose nucleotide sequences of glutamine synthetasegenes which confer resistance to herbicides such as L-phosphinothricin.The nucleotide sequence of a phosphinothricin-acetyl-transferase gene isprovided in European application No. 0 242 246 to Leemans et al.,DeGreef et al., Bio/Technology 7:61 (1989), describe the production oftransgenic plants that express chimeric bar genes coding forphosphinothricin acetyl transferase activity. Exemplary of genesconferring resistance to phenoxy proprionic acids and cyclohexones, suchas sethoxydim and haloxyfop are the Acc1-S1, Acc1-S2 and Acc1-S3 genesdescribed by Marshall et al., Theor. Appl. Genet. 83:435 (1992).

C. An herbicide that inhibits photosynthesis, such as a triazine (psbAand gs+ genes) and a benzonitrile (nitrilase gene). Przibilla et al.,Plant Cell 3:169 (1991), describe the transformation of Chlamydomonaswith plasmids encoding mutant psbA genes. Nucleotide sequences fornitrilase genes are disclosed in U.S. Pat. No. 4,810,648 to Stalker, andDNA molecules containing these genes are available under ATCC AccessionNos. 53435, 67441, and 67442. Cloning and expression of DNA coding for aglutathione S-transferase is described by Hayes et al., Biochem. J.285:173 (1992).

D. Acetohydroxy acid synthase, which has been found to make plants thatexpress this enzyme resistant to multiple types of herbicides, has beenintroduced into a variety of plants. See Hattori et al., Mol. Gen.Genet. 246:419, 1995. Other genes that confer tolerance to herbicidesinclude a gene encoding a chimeric protein of rat cytochrome P4507A1 andyeast NADPH-cytochrome P450 oxidoreductase (Shiota et al., PlantPhysiol., 106:17, 1994), genes for glutathione reductase and superoxidedismutase (Aono et al., Plant Cell Physiol. 36:1687, 1995), and genesfor various phosphotransferases (Datta et al., Plant Mol. Biol. 20:619,1992).

E. Protoporphyrinogen oxidase (PPO; protox) is the target of thePPO-inhibitor class of herbicides; a PPO-inhibitor resistant PPO genewas recently identified in Amaranthus tuberculatus (Patzoldt et al.,PNAS, 103(33):12329-2334, 2006). PPO is necessary for the production ofchlorophyll, which is necessary for all plant survival. The protoxenzyme serves as the target for a variety of herbicidal compounds. Theseherbicides also inhibit growth of all the different species of plantspresent, causing their total destruction. The development of plantscontaining altered protox activity which are resistant to theseherbicides are described in U.S. Pat. Nos. 6,288,306, 6,282,837,5,767,373, and International Publication WO 01/12825.

F. Genes that confer resistance to auxin or synthetic auxin herbicides.For example an aryloxyalkanoate dioxygenase (AAD) gene may conferresistance to arlyoxyalkanoate herbicides, such as 2,4-D, as well aspyridyloxyacetate herbicides, such as described in U.S. Pat. No.8,283,522, and US2013/0035233. In other examples, a dicambamonooxygenase (DMO) is used to confer resistance to dicamba. Otherpolynucleotides of interest related to auxin herbicides and/or usesthereof include, for example, the descriptions found in U.S. Pat. Nos.8,119,380; 7,812,224; 7,884,262; 7,855,326; 7,939,721; 7,105,724;7,022,896; 8,207,092; US2011/067134; and US2010/0279866. Any of theabove listed herbicide genes (1-6) can be introduced into the claimedrice cultivar through a variety of means including, but not limited to,transformation and crossing.

3. Genes that Confer or Contribute to a Value-Added Trait, Such as:

A. Increased iron content of the rice, for example by transforming aplant with a soybean ferritin gene as described in Goto et al., ActaHorticulturae. 2000, 521, 101-109.

B. Decreased nitrate content of leaves, for example by transforming arice with a gene coding for a nitrate reductase. See for example Curtiset al., Plant Cell Report. 1999, 18:11, 889-896.

C. Increased sweetness of the rice by transferring a gene coding formonellin that elicits a flavor 100,000 times sweeter than sugar on amolar basis. See Penarrubia et al., Biotechnology. 1992, 10:5, 561-564.

D. Modified fatty acid metabolism, for example, by transforming a plantwith an antisense gene of stearyl-ACP desaturase to increase stearicacid content of the plant. See Knultzon et al., Proc. Natl. Acad. Sci.USA 89:2625 (1992).

E. Modified carbohydrate composition effected, for example, bytransforming plants with a gene coding for an enzyme that alters thebranching pattern of starch. See Shiroza et al., J. Bacteriol. 170:810(1988) (nucleotide sequence of Streptococcus mutantsfructosyltransferase gene), Steinmetz et al., Mol. Gen. Genet. 20:220(1985) (nucleotide sequence of Bacillus subtilis levansucrase gene), Penet al., Bio/Technology 10:292 (1992) (production of transgenic plantsthat express Bacillus lichenifonnis α-amylase), Elliot et al., PlantMolec. Biol. 21:515 (1993) (nucleotide sequences of tomato invertasegenes), Søgaard et al., J. Biol. Chem. 268:22480 (1993) (site-directedmutagenesis of barley α-amylase gene), and Fisher et al., Plant Physiol.102:1045 (1993) (maize endosperm starch branching enzyme II).

F. Altered antioxidant content or composition, such as alteration oftocopherol or tocotrienols. See, for example, U.S. Pat. Nos. 6,787,683,7,154,029, WO 00/68393 (involving the manipulation of antioxidant levelsthrough alteration of a phytl prenyl transferase (ppt)); WO 03/082899(through alteration of a homogentisate geranyl geranyl transferase(hggt)).

4. Genes that Control Male-Sterility

A. Introduction of a deacetylase gene under the control of atapetum-specific promoter and with the application of the chemicalN-Ac-PPT. See international publication WO 01/29237.

B. Introduction of various stamen-specific promoters. See internationalpublications WO 92/13956 and WO 92/13957.

C. Introduction of the barnase and the barstar genes. See Paul et al.,Plant Mol. Biol. 19:611-622, 1992).

For additional examples of nuclear male and female sterility systems andgenes, see also, U.S. Pat. Nos. 5,859,341, 6,297,426, 5,478,369,5,824,524, 5,850,014, and 6,265,640, all of which are herebyincorporated by reference.

5. Genes that Affect Abiotic Stress Resistance

Genes that affect abiotic stress resistance (including but not limitedto flowering, seed development, enhancement of nitrogen utilizationefficiency, altered nitrogen responsiveness, drought resistance ortolerance, cold resistance or tolerance, high or low light intensity,and salt resistance or tolerance) and increased yield under stress. Forexample, see: WO 00/73475 where water use efficiency is altered throughalteration of malate; U.S. Pat. Nos. 5,892,009, 5,965,705, 5,929,305,5,891,859, 6,417,428, 6,664,446, 6,706,866, 6,717,034, 6,801,104, WO2000/060089, WO 2001/026459, WO 2001/035725, WO 2001/034726, WO2001/035727, WO 2001/036444, WO 2001/036597, WO 2001/036598, WO2002/015675, WO 2002/017430, WO 2002/077185, WO 2002/079403, WO2003/013227, WO 2003/013228, WO 2003/014327, WO 2004/031349, WO2004/076638, WO 98/09521, and WO 99/38977 describing genes, includingCBF genes and transcription factors effective in mitigating the negativeeffects of freezing, high salinity, and drought on plants, as well asconferring other positive effects on plant phenotype; U.S. Publ. No.2004/0148654 and WO 01/36596, where abscisic acid is altered in plantsresulting in improved plant phenotype, such as increased yield and/orincreased tolerance to abiotic stress; WO 2000/006341, WO 04/090143,U.S. Pat. Nos. 7,531,723 and 6,992,237, where cytokinin expression ismodified resulting in plants with increased stress tolerance, such asdrought tolerance, and/or increased yield. See also, WO 02/02776, WO2003/052063, JP 2002281975, U.S. Pat. No. 6,084,153, WO 01/64898, andU.S. Pat. Nos. 6,177,275 and 6,107,547 (enhancement of nitrogenutilization and altered nitrogen responsiveness). For ethylenealteration, see, U.S. Publ. Nos. 2004/0128719, 2003/0166197, and WO2000/32761. For plant transcription factors or transcriptionalregulators of abiotic stress, see, e.g., U.S. Publ. Nos. 2004/0098764 or2004/0078852.

Other genes and transcription factors that affect plant growth andagronomic traits, such as yield, flowering, plant growth, and/or plantstructure, can be introduced or introgressed into plants. See, e.g., WO97/49811 (LHY), WO 98/56918 (ESD4), WO 97/10339, U.S. Pat. No. 6,573,430(TFL), 6,713,663 (FT), 6,794,560, 6,307,126 (GAI), WO 96/14414 (CON), WO96/38560, WO 01/21822 (VRN1), WO 00/44918 (VRN2), WO 99/49064 (GI), WO00/46358 (FM), WO 97/29123, WO 99/09174 (D8 and Rht), WO 2004/076638,and WO 004/031349 (transcription factors).

Tissue Culture

Further reproduction of the cultivar can occur by tissue culture andregeneration. Tissue culture of various tissues of plants andregeneration of plants therefrom is well known and widely published. Forexample, see Teng et al., HortScience. 1992, 27:9, 1030-1032 Teng etal., HortScience. 1993, 28:6, 669-1671, Zhang et al., Journal ofGenetics and Breeding. 1992, 46:3, 287-290, Webb et al., Plant CellTissue and Organ Culture. 1994, 38:1, 77-79, Curtis et al., Journal ofExperimental Botany. 1994, 45:279, 1441-1449, Nagata et al., Journal forthe American Society for Horticultural Science. 2000, 125:6, 669-672,Komatsuda, T. et al., Crop Sci. 31:333-337 (1991); Stephens, P. A., etal., Theor. Appl. Genet. (1991) 82:633-635; Komatsuda, T. et al., PlantCell, Tissue and Organ Culture, 28:103-113 (1992); Dhir, S. et al.,Plant Cell Reports (1992) 11:285-289; Pandey, P. et al., Japan J. Breed.42:1-5 (1992); and Shetty, K., et al., Plant Science 81:245-251 (1992);as well as U.S. Pat. No. 5,024,944 issued Jun. 18, 1991 to Collins etal., and U.S. Pat. No. 5,008,200 issued Apr. 16, 1991 to Ranch et al.Thus, another aspect of this invention is to provide cells which upongrowth and differentiation produce rice plants having all of thephysiological and morphological characteristics of rice varietyCalaroma-201.

As used herein, the term “tissue culture” indicates a compositioncomprising isolated cells of the same or a different type or acollection of such cells organized into parts of a plant. Exemplarytypes of tissue cultures are protoplasts, calli, plant clumps, and plantcells that can generate tissue culture that are intact in plants orparts of plants, such as embryos, hypocotyls, pollen, flowers, seeds,leaves, stems, roots, root tips, pistils, anthers, meristematic cellsand the like. Means for preparing and maintaining plant tissue cultureare well known in the art. By way of example, a tissue culturecomprising organs has been used to produce regenerated plants. U.S. Pat.Nos. 5,959,185; 5,973,234 and 5,977,445 describe certain techniques, thedisclosures of which are incorporated herein by reference.

The present invention contemplates a rice plant regenerated from atissue culture of a variety (e.g., Calaroma-201) or hybrid plant of thepresent invention. As is well known in the art, tissue culture of ricecan be used for the in vitro regeneration of a rice plant. Tissueculture of various tissues of rice and regeneration of plants therefromis well known and widely published. For example, reference may be had toChu, Q. R., et al., (1999) “Use of bridging parents with high antherculturability to improve plant regeneration and breeding value in rice”,Rice Biotechnology Quarterly 38:25-26; Chu, Q. R., et al., (1998), “Anovel plant regeneration medium for rice anther culture of Southern U.S.crosses”, Rice Biotechnology Quarterly 35:15-16; Chu, Q. R., et al.,(1997), “A novel basal medium for embryogenic callus induction ofSouthern US crosses”, Rice Biotechnology Quarterly 32:19-20; and Oono,K., “Broadening the Genetic Variability By Tissue Culture Methods”, Jap.J. Breed. 33 (Suppl.2), 306-307, illus. 1983. Thus, another aspect ofthis invention is to provide cells which upon growth and differentiationproduce rice plants having the physiological and morphologicalcharacteristics of variety Calaroma-201.

Duncan, et al., Planta 165:322-332 (1985) reflects that 97% of theplants cultured that produced callus were capable of plant regeneration.Subsequent experiments with both cultivars and hybrids produced 91%regenerable callus that produced plants. In a further study in 1988,Songstad, et al., Plant Cell Reports 7:262-265 (1988), reports severalmedia additions that enhance regenerability of callus of two cultivars.Other published reports also indicated that “non-traditional” tissuesare capable of producing somatic embryogenesis and plant regeneration.K. P. Rao et al., Maize Genetics Cooperation Newsletter, 60:64-65(1986), refers to somatic embryogenesis from glume callus cultures andB. V. Conger, et al., Plant Cell Reports, 6:345-347 (1987) indicatessomatic embryogenesis from the tissue cultures of corn leaf segments.Thus, it is clear from the literature that the state of the art is suchthat these methods of obtaining plants are routinely used and have avery high rate of success. Thus, another aspect of this invention is toprovide cells which upon growth and differentiation produce rice plantshaving the physiological and morphological characteristics of ricecultivar Calaroma-201.

The utility of rice cultivar Calaroma-201 also extends to crosses withother species. Commonly, suitable species will be of the familyGraminaceae, and especially of the genera Zea, Tripsacum, Croix,Schlerachne, Polytoca, Chionachne, and Trilobachne, of the tribeMaydeae.

Uses of Rice Cultivar Calaroma-201

The seed of rice cultivar Calaroma-201, the plant produced from thecultivar seed, the hybrid rice plant produced from the crossing of thecultivar, hybrid seed, and various parts of the hybrid rice plant andtransgenic versions of the foregoing, can be utilized for human food,livestock feed, and as a raw material in industry. As a non-limitingexample, rice cultivar Calaroma-201 can be used as a commodity plantproduct for rice, meal, flour, oil, film, packaging, and nutraceuticalproducts.

Tables

Table 2 shows the combined results of University of CaliforniaCooperative Extension Statewide Yield Tests for maturity groups from2015 to 2017 for rice cultivar Calaroma-201 (experimental designation18Y84) compared to long grains A-202 and L-206. The replicated testplots were 10×20 foot plots and tests were performed in commercialgrowers' fields at RES in Biggs, Calif., Colusa County, Butte County,Sutter County, and Yuba County. Column 1 shows the entry name, column 2shows the grain yield in pounds per acre (lbs./acre), column 3 shows theseedling vigor score on a scale of 1 to 5, column 4 shows the days to50% heading, column 5 shows the percent (%) lodging and column 6 theplant height in centimeters (cm). Seedling vigor score is a visual scorewhere a score of 1 is poor and a score of 5 is excellent.

TABLE 2 Grain Seedling Plant Yield Vigor Days to Lodging Height Entry(lbs./a) (1-5) Heading (%) (cm) L-206 9310 4.8 81 28 90 A-202 8890 4.985 27 99 Calaroma-201 9450 4.9 86 26 91

As shown in Table 2, rice cultivar Calaroma-201 had a higher grain yieldthan L-206 and A-202. Additionally, Calaroma-201 was 5 days later to 50%heading than L-206 and was 8 cm shorter than A-202.

Table 3 shows the results of the University of California CooperativeExtension Statewide Yield Tests for the Very Early Group from 2015 to2017 for rice cultivar Calaroma-201 compared to long grains A-202 andL-206. Column 1 shows the site location, column 2 shows the entry name,column 3 shows the yield in pounds per acre (lbs./acre), column 4 showsthe seedling vigor score on a scale of 1 to 5, column 5 shows the daysto 50% heading, column 6 shows the percent (%) lodging and column 7shows the plant height in centimeters (cm). Seedling vigor score is avisual score where a score of 1 is poor and a score of 5 is excellent.

TABLE 3 Grain Seedling Plant Yield Vigor Days to Lodging Height LocationEntry (lbs./a) (1-5) Heading (%) (cm) Biggs L-206 9851 4.8 70 13 89 2017A-202 7893 4.9 72 5 100 Calaroma-201 10814 4.9 75 3 93 Yolo L-206 92504.7 80 6 92 2017 A-202 9408 4.8 84 1 104 Calaroma-201 9555 4.9 86 1 91Yolo site 2 L-206 6859 4.8 93 1 78 2017 A-202 6259 4.8 100 1 85Calaroma-201 7048 4.8 97 1 77 Sutter L-206 8576 4.7 81 3 86 2017 A-2028824 4.8 83 1 94 Calaroma-201 8620 4.7 85 6 83

As shown in Table 3, rice cultivar Calaroma-201 had the highest grainyield at all locations except Sutter and had longer days to 50% headingat all locations except Yolo site 2. Additionally, Calaroma-201 wasshorter than A-202 at all locations.

Table 4 shows the results of the University of California CooperativeExtension Statewide Yield Tests for the Early Group from 2015 and 2017for rice cultivar Calaroma-201 compared to long grains A-202 and L-206.Column 1 shows the site location, column 2 shows the entry name, column3 shows the yield in pounds per acre (lbs./acre), column 4 shows theseedling vigor score on a scale of 1 to 5, column 5 shows the days to50% heading, column 6 shows the percent (%) lodging and column 7 showsthe plant height in centimeters (cm). Seedling vigor score is a visualscore where a score of 1 is poor and a score of 5 is excellent.

TABLE 4 Grain Seedling Plant Yield Vigor Days to Lodging Height LocationEntry (lbs./a) (1-5) Heading (%) (cm) Biggs L-206 10298 4.7 76 12 87A-202 9507 4.9 79 23 95 Calaroma-201 10528 4.8 81 15 88 Butte L-206 97164.8 80 41 95 A-202 9576 4.9 86 35 101 Calaroma-201 9866 5.0 88 28 90Yuba L-206 8725 4.9 81 62 89 A-202 8404 4.9 86 49 97 Calaroma-201 86915.0 89 31 90 Colusa L-206 9206 4.9 86 3 92 A-202 9536 4.9 91 1 100Calaroma-201 9763 4.7 94 6 94

As shown in Table 4, rice cultivar Calaroma-201 had the highest grainyield at all locations except Yuba and had longer days to 50% heading atall locations. Additionally, Calaroma-201 was shorter than A-202 at alllocations.

Table 5 shows the results of the University of California CooperativeExtension Statewide Yield Tests for the Intermediate Group from 2016 and2017 for rice cultivar Calaroma-201 compared to long grains A-202 andL-206. Column 1 shows the site location, column 2 shows the entry name,column 3 shows the yield in pounds per acre (lbs/acre), column 4 showsthe seedling vigor score on a scale of 1 to 5, column 5 shows the daysto 50% heading, column 6 shows the percent (%) lodging and column 7shows the plant height in centimeters (cm). Seedling vigor score is avisual score where a score of 1 is poor and a score of 5 is excellent.

TABLE 5 Grain Seedling Plant Yield Vigor Days to Lodging Height LocationEntry Name (lbs./a) (1-5) Heading (%) (cm) Biggs L-206 10506 4.8 75 8 93A-202 10197 4.9 79 6 100 Calaroma-201 10724 4.9 82 2 93 Glenn L-206 84244.7 82 64 96 A-202 7157 4.9 87 74 103 Calaroma-201 8350 4.9 90 74 101Butte L-206 9254 4.9 85 46 91 A-202 8743 4.9 88 46 100 Calaroma-201 96314.9 90 43 91

As shown in Table 5, rice cultivar Calaroma-201 had the highest grainyield at Biggs and Butte, and longer days to 50% heading at alllocations. Additionally, Calaroma-201 was shorter than A-202 at alllocations.

Table 6 shows the grain measurements for rice cultivar Calaroma-201compared to long grains A-202 and L-206. Samples were collected from RESin Biggs, Calif. in 2016-2017. Column 1 shows the year, column 2 theentry name, columns 3-5, 6-8, and 9-11 show length in millimeters (mm),width in millimeters (mm) and 1000 kernel weight in grams (g) for paddy,brown, and milled rice, respectively, and column 12 shows thelength/width (L/W) ratio for the milled rice.

TABLE 6 Paddy Rice Brown Rice Milled Rice 1000 1000 1000 Length Widthseed Length Width kernel Length Width kernel L/W Year Entry (mm) (mm)wt. (mm) (mm) wt. (mm) (mm) wt. Ratio 2016 L-206 7.00 2.12 19.34 3.30A-202 7.07 2.28 21.57 3.11 Calaroma-201 7.13 2.06 19.38 3.47 2017 L-20610.04 2.51 26.37 7.90 2.18 21.51 7.19 2.12 20.54 3.39 A-202 10.01 2.5830.31 7.90 2.37 24.74 7.39 2.31 22.97 3.20 Calaroma-201 9.93 2.40 27.297.98 2.14 22.81 7.41 2.01 20.05 3.69 Mean L-206 10.04 2.51 26.37 7.902.18 21.51 7.10 2.12 19.94 3.35 A-202 10.01 2.58 30.31 7.90 2.37 24.747.23 2.30 22.27 3.15 Calaroma-201 9.93 2.40 27.29 7.98 2.14 22.81 7.272.04 19.72 3.58

As shown in Table 6, rice cultivar Calaroma-201 is more slender than theother two long grain cultivars.

To evaluate the milling characteristics of a rice line, milling sampleswere harvested once or twice on a weekly basis starting when grains areabove 22% moisture down to when grain are about 15% moisture. Samplesare milled and measured for % Head rice and % Total milled rice. Table 7contains the milling (total milled and head rice percentage) of ricecultivar Calaroma-201 compared to rice cultivars L-206 and A-202 acrossharvest moistures from 2015 to 2017 taken from milling plots at RES.Column 1 show the entry name, columns 2, 5 and 8 show the harvestmoistures in percent (%), columns 3, 6 and 9 show the % Head rice, andcolumns 4, 8 and 10 show the % Total milled rice for 2015-2017,respectively.

TABLE 7 2015 2016 2017 Harvest % % Harvest % % Harvest % % Entry MC (%)Head Total MC (%) Head Total MC (%) Head Total L-206 21.3 59 69 20.5 6369 22.4 60 68 20.4 57 69 20.1 63 70 21.9 55 64 20.3 60 70 19.5 63 7120.7 60 70 18.3 62 70 19.3 65 71 20.0 58 68 18.2 56 68 19.0 64 71 19.659 68 16.8 59 70 17.7 63 70 19.3 62 69 16.6 62 69 18.6 57 68 16.2 63 7217.6 61 69 15.6 65 71 15.3 62 69 15.3 62 70 15.2 55 67 A-202 21.1 60 6918.0 63 70 22.6 53 66 21.0 60 68 17.7 63 71 21.6 61 69 20.8 60 67 16.356 69 21.1 64 70 16.8 53 66 20.2 63 70 16.6 60 71 19.8 60 68 16.3 48 6518.7 62 71 14.4 39 63 17.8 65 71 Calaroma-201 20.4 60 67 22.0 60 67 22.161 67 15.4 57 67 20.0 59 67 19.6 62 68 19.3 58 67 19.4 63 68 17.5 59 6718.4 65 70 17.2 58 70 17.9 66 70 17.1 48 61 17.7 63 69 16.4 55 67 16.561 67 15.3 43 65

Table 8 summarizes the overall milling performance of rice cultivarsCalaroma-201, L-206 and A-202 harvested under high moisture (>21%),optimum moisture (19-21%) and low moisture (<19%). Column 1 shows theentry name, column 2 shows the milling performance under high moisture(>21%), column 3 shows the milling performance under optimum moisture(19-21%), and column 4 shows the milling performance under low moisture(<19%).

TABLE 8 % Moisture Content at Harvest More than Less than Entry 21%19-21% 19% Calaroma-201 60/67 60/67 58/67 A-202 60/68 61/68 56/68 L-20658/67 61/70 61/70

As shown in Table 8, the percentage of total rice of Calaroma-201 waslower compared to the checks.

Table 9 summarizes the milled rice apparent amylose content, proteinpercentage, and gel type of rice cultivars Calaroma-201 (experimentaldesignation 18Y84), L-206 and A-202 taken from 2015 to 2016 data throughindependent external evaluation (USDA and California Wheat Commission).Column 1 shows the year, column 2 shows the entry name, column 3 showsapparent amylose content percent (%), column 4 shows the percent (%)protein and column 5 shows the gelatinization temperatureclassification.

TABLE 9 Apparent Amylose Protein Gelatinization Year Entry (%) (%)Temperature 2015 L-206 23.56 7.15 Intermediate A-202 23.75 4.74Intermediate Calaroma-201 16.56 5.93 Low 2016 L-206 21.25 7.75Intermediate A-202 21.00 6.43 Intermediate Calaroma-201 14.95 6.11 LowMean L-206 22.41 7.45 Intermediate A-202 22.38 5.59 IntermediateCalaroma-201 15.76 6.02 Low

As shown in Table 9, rice cultivar Calaroma-201 has a lower amylosecontent than L-206 and A-202. Calaroma-201 also has a low gelatinizationtemperature, whereas L-206 and A-202 have an intermediate gelatinizationtemperature. These characteristics cause the rice of Calaroma-201 tocook softer and stickier compared to conventional long grains L-206 orA-202, and is a cooking characteristic of Thai Jasmine type rice.

Table 10 shows the RVA values of rice cultivars Calaroma-201, L-206 andA-202 collected at RES. Column 1 shows the year, column 2 the entryname, column 3 shows the peak, column 4 shows the trough, column 5 showsthe breakdown, column 6 shows the final viscosity and column 7 shows thesetback.

TABLE 10 Break Final Year Entry Peak Trough down Visc. Setback 2015L-206 269 158 112 305 36 A-202 217 120 97 245 28 Calaroma-201 282 136146 241 −41 2016 L-206 238 132 106 271 33 A-202 223 134 89 267 43Calaroma-201 282 133 149 243 −38 2017-A L-206 258 139 120 283 25 A-202238 123 115 257 19 Calaroma-201 259 120 139 218 −41 2017-B L-206 268 140128 282 14 A-202 275 133 142 277 3 Calaroma-201 287 130 157 234 −542017-C L-206 248 135 113 283 35 A-202 261 132 129 268 7 Calaroma-201 262124 139 221 −41 Mean L-206 256 141 116 285 28 A-202 243 128 115 263 20Calaroma-201 274 128 146 231 −43

As shown in Table 10, the RVA of rice cultivar Calaroma-201 ischaracterized by having higher peak viscosity and breakdown values,lower final viscosity values, and a negative setback when compared toL-206 and A-202, indicating softer and stickier cooking characteristicsof Calaroma-201.

The use of the terms “a” and “an” and “the” and similar referents in thecontext of describing the invention (especially in the context of thefollowing claims) are to be construed to cover both the singular and theplural, unless otherwise indicated herein or clearly contradicted bycontext. The terms “comprising,” “having,” “including,” and “containing”are to be construed as open-ended terms (i.e., meaning “including, butnot limited to,”) unless otherwise noted. Recitation of ranges of valuesherein are merely intended to serve as a shorthand method of referringindividually to each separate value falling within the range, unlessotherwise indicated herein, and each separate value is incorporated intothe specification as if it were individually recited herein. Forexample, if the range 10-15 is disclosed, then 11, 12, 13, and 14 arealso disclosed. All methods described herein can be performed in anysuitable order unless otherwise indicated herein or otherwise clearlycontradicted by context. The use of any and all examples, or exemplarylanguage (e.g., “such as”) provided herein, is intended merely to betterilluminate the invention and does not pose a limitation on the scope ofthe invention unless otherwise claimed. No language in the specificationshould be construed as indicating any non-claimed element as essentialto the practice of the invention.

DEPOSIT INFORMATION

A deposit of the California Cooperative Rice Research Foundation, Inc.proprietary rice cultivar Calaroma-201 disclosed above and recited inthe appended claims has been made with the American Type CultureCollection (ATCC), 10801 University Boulevard, Manassas, Va. 20110 underthe terms of the Budapest Treaty. The date of deposit was Sep. 20, 2018.The deposit of 2,500 seeds was taken from the same deposit maintained byCalifornia Cooperative Rice Research Foundation, Inc. since prior to thefiling date of this application. All restrictions will be irrevocablyremoved upon granting of a patent, and the deposit is intended to meetall of the requirements of 37 C.F.R. §§ 1.801-1.809. The ATCC AccessionNumber is PTA-125255. The deposit will be maintained in the depositoryfor a period of thirty years, or five years after the last request, orfor the enforceable life of the patent, whichever is longer, and will bereplaced as necessary during that period.

While a number of exemplary aspects and embodiments have been discussedabove, those of skill in the art will recognize certain modifications,permutations, additions and sub-combinations thereof. It is thereforeintended that the following appended claims and claims hereafterintroduced are interpreted to include all such modifications,permutations, additions and sub-combinations as are within their truespirit and scope.

What is claimed is:
 1. A seed of rice cultivar Calaroma-201, wherein arepresentative sample of seed of said cultivar has been deposited underATCC Accession No. PTA-125255.
 2. A rice plant, or a plant part thereof,produced by growing the seed of claim
 1. 3. A tissue culture of cells orprotoplasts produced from the plant of claim 2, wherein said cells orprotoplasts of the tissue culture are produced from a plant partselected from the group consisting of leaf, pollen, ovule, embryo,cotyledon, hypocotyl, meristematic cell, root, root tip, pistil, anther,flower, stem, seed, glumes and panicle.
 4. A rice plant regenerated fromthe tissue culture of claim 3, wherein the plant has all of themorphological and physiological characteristics of rice cultivarCalaroma-201.
 5. A method for producing an F₁ hybrid rice seed, whereinthe method comprises crossing the plant of claim 2 with a different riceplant and harvesting the resultant F₁ hybrid rice seed.
 6. A hybrid riceseed produced by the method of claim
 5. 7. A hybrid rice plant producedby growing said hybrid rice seed of claim
 6. 8. A method of producing anherbicide resistant rice plant, wherein the method comprisestransforming the rice plant of claim 2 with a transgene, wherein thetransgene confers resistance to an herbicide selected from the groupconsisting of glyphosate, sulfonylurea, imidazolinone, dicamba,glufosinate, phenoxy proprionic acid, L-phosphinothricin, cyclohexone,cyclohexanedione, triazine, benzonitrile, protoporphyrinogen oxidase(PPO)-inhibitor herbicides and broxynil.
 9. An herbicide resistant riceplant produced by the method of claim
 8. 10. A method of producing apest or insect resistant rice plant, wherein the method comprisestransforming the rice plant of claim 2 with a transgene that conferspest or insect resistance.
 11. A pest or insect resistant rice plantproduced by the method of claim
 10. 12. The rice plant of claim 11,wherein the transgene encodes a Bacillus thuringiensis endotoxin.
 13. Amethod of producing a disease resistant rice plant, wherein the methodcomprises transforming the rice plant of claim 2 with a transgene thatconfers disease resistance.
 14. A disease resistant rice plant producedby the method of claim
 13. 15. A method of producing a rice plant withmodified fatty acid metabolism or modified carbohydrate metabolism,wherein the method comprises transforming the rice plant of claim 2 witha transgene encoding a protein selected from the group consisting offructosyltransferase, levansucrase, alpha-amylase, invertase and starchbranching enzyme or DNA encoding an antisense of stearyl-ACP desaturase.16. A rice plant having modified fatty acid metabolism or modifiedcarbohydrate metabolism produced by the method of claim
 15. 17. A methodof introducing a desired trait into rice cultivar Calaroma-201, whereinthe method comprises: (a) crossing a Calaroma-201 plant, wherein arepresentative sample of seed was deposited under ATCC Accession No.PTA-125255, with a plant of another rice cultivar that comprises adesired trait to produce progeny plants, wherein the desired trait isselected from the group consisting of male sterility, herbicideresistance, pest or insect resistance, abiotic stress tolerance,modified fatty acid metabolism, modified carbohydrate metabolism,enhanced nutritional quality, modified protein content, enhanced plantquality and resistance to bacterial disease, fungal disease or viraldisease; (b) selecting one or more progeny plants that have the desiredtrait; (c) backcrossing the selected progeny plants with theCalaroma-201 plants to produce backcross progeny plants; (d) selectingfor backcross progeny plants that have the desired trait; and (e)repeating steps (c) and (d) two or more times to produce selected thirdor higher backcross progeny plants that comprise the desired trait. 18.A plant produced by the method of claim 17, wherein the plant has thedesired trait and otherwise all of the physiological and morphologicalcharacteristics of rice cultivar Calaroma-201.
 19. The plant of claim18, wherein the desired trait is herbicide resistance and the resistanceis conferred to an herbicide selected from the group consisting ofglyphosate, sulfonylurea, imidazolinone, dicamba, glufosinate, phenoxyproprionic acid, L-phosphinothricin, cyclohexone, cyclohexanedione,triazine, benzonitrile, protoporphyrinogen oxidase (PPO)-inhibitorherbicides and broxynil.
 20. The plant of claim 18, wherein the desiredtrait is insect resistance and the insect resistance is conferred by atransgene encoding a Bacillus thuringiensis endotoxin.
 21. The plant ofclaim 18, wherein the desired trait is modified fatty acid metabolism ormodified carbohydrate metabolism and said desired trait is conferred bya nucleic acid encoding a protein selected from the group consisting offructosyltransferase, levansucrase, alpha-amylase, invertase and starchbranching enzyme or DNA encoding an antisense of stearyl-ACP desaturase.22. The plant of claim 18, wherein the desired trait is abiotic stresstolerance and said desired trait modifies tolerance to drought,flooding, salinity, or temperature change.
 23. The method of claim 5,wherein the method further comprises: (a) crossing a plant grown fromsaid F₁ hybrid rice seed with itself or a different rice plant toproduce a seed of a progeny plant of a subsequent generation; (b)growing a progeny plant of a subsequent generation from said seed of aprogeny plant of a subsequent generation and crossing the progeny plantof a subsequent generation with itself or a second plant to produce aprogeny plant of a further subsequent generation; and (c) repeatingsteps (a) and (b) using said progeny plant of a further subsequentgeneration from step (b) in place of the plant grown from said F₁ hybridrice seed in step (a), wherein steps (a) and (b) are repeated withsufficient inbreeding to produce an inbred rice plant derived from therice cultivar Calaroma-201.
 24. The method of claim 23, furthercomprising crossing said inbred rice plant derived from the ricecultivar Calaroma-201 with a plant of a different genotype to produce aseed of a hybrid rice plant derived from the rice cultivar Calaroma-201.25. A method of introducing the head rice stability trait of ricecultivar Calaroma-201 into another rice cultivar, wherein the methodcomprises crossing a Calaroma-201 plant, wherein a representative sampleof seed is deposited under ATCC Accession No. PTA-125255, with a plantof another rice cultivar and selecting for progeny plants that have headrice stability.
 26. A method of producing a genetically modified riceplant, wherein the method comprises gene conversion, genome editing, RNAinterference or gene silencing of the plant of claim
 2. 27. Agenetically modified rice plant produced by the method of claim 26,wherein said plant comprises said gene conversion, genome editing, RNAinterference or gene silencing and otherwise comprises all of thephysiological and morphological characteristics of rice cultivarCalaroma-201.
 28. A method of producing a commodity plant product,comprising obtaining the plant of claim 2, or a part thereof, andproducing the commodity plant product from said plant or plant partthereof, wherein said commodity plant product is selected from the groupconsisting of rice, meal, flour, oil, film, packaging, and nutraceuticalproduct.